diff --git a/cmd/pd-server/main.go b/cmd/pd-server/main.go
index 21e6d5ca0e0..ea5c26b00fe 100644
--- a/cmd/pd-server/main.go
+++ b/cmd/pd-server/main.go
@@ -24,10 +24,11 @@ import (
 	grpcprometheus "github.com/grpc-ecosystem/go-grpc-prometheus"
 	"github.com/pingcap/errors"
 	"github.com/pingcap/log"
+	"github.com/spf13/cobra"
 	"github.com/tikv/pd/pkg/autoscaling"
-	bs "github.com/tikv/pd/pkg/basicserver"
 	"github.com/tikv/pd/pkg/dashboard"
 	"github.com/tikv/pd/pkg/errs"
+	tso "github.com/tikv/pd/pkg/mcs/tso/server"
 	"github.com/tikv/pd/pkg/swaggerserver"
 	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/pkg/utils/metricutil"
@@ -41,43 +42,83 @@ import (
 )
 
 func main() {
-	ctx, cancel, svr := createServerWrapper(os.Args[1:])
-
-	sc := make(chan os.Signal, 1)
-	signal.Notify(sc,
-		syscall.SIGHUP,
-		syscall.SIGINT,
-		syscall.SIGTERM,
-		syscall.SIGQUIT)
-
-	var sig os.Signal
-	go func() {
-		sig = <-sc
-		cancel()
-	}()
+	rootCmd := &cobra.Command{
+		Use:   "pd-server",
+		Short: "Placement Driver server",
+		Run:   createServerWrapper,
+	}
 
-	if err := svr.Run(); err != nil {
-		log.Fatal("run server failed", errs.ZapError(err))
+	rootCmd.Flags().BoolP("version", "V", false, "print version information and exit")
+	rootCmd.Flags().StringP("config", "", "", "config file")
+	rootCmd.Flags().BoolP("config-check", "", false, "check config file validity and exit")
+	rootCmd.Flags().StringP("name", "", "", "human-readable name for this pd member")
+	rootCmd.Flags().StringP("data-dir", "", "", "path to the data directory (default 'default.${name}')")
+	rootCmd.Flags().StringP("client-urls", "", "http://127.0.0.1:2379", "url for client traffic")
+	rootCmd.Flags().StringP("advertise-client-urls", "", "", "advertise url for client traffic (default '${client-urls}')")
+	rootCmd.Flags().StringP("peer-urls", "", "http://127.0.0.1:2379", "url for peer traffic")
+	rootCmd.Flags().StringP("advertise-peer-urls", "", "", "advertise url for peer traffic (default '${peer-urls}')")
+	rootCmd.Flags().StringP("initial-cluster", "", "", "initial cluster configuration for bootstrapping, e,g. pd=http://127.0.0.1:2380")
+	rootCmd.Flags().StringP("join", "", "", "join to an existing cluster (usage: cluster's '${advertise-client-urls}'")
+	rootCmd.Flags().StringP("metrics-addr", "", "", "prometheus pushgateway address, leaves it empty will disable prometheus push")
+	rootCmd.Flags().StringP("log-level", "L", "info", "log level: debug, info, warn, error, fatal (default 'info')")
+	rootCmd.Flags().StringP("log-file", "", "", "log file path")
+	rootCmd.Flags().StringP("cacert", "", "", "path of file that contains list of trusted TLS CAs")
+	rootCmd.Flags().StringP("cert", "", "", "path of file that contains X509 certificate in PEM format")
+	rootCmd.Flags().StringP("key", "", "", "path of file that contains X509 key in PEM format")
+	rootCmd.Flags().BoolP("force-new-cluster", "", false, "force to create a new one-member cluster")
+	rootCmd.AddCommand(NewServiceCommand())
+
+	rootCmd.SetOutput(os.Stdout)
+	if err := rootCmd.Execute(); err != nil {
+		rootCmd.Println(err)
+		os.Exit(1)
 	}
+}
 
-	<-ctx.Done()
-	log.Info("Got signal to exit", zap.String("signal", sig.String()))
+// NewServiceCommand returns the service command.
+func NewServiceCommand() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "service <tso>",
+		Short: "Run a service",
+	}
+	cmd.AddCommand(NewTSOServiceCommand())
+	return cmd
+}
 
-	svr.Close()
-	switch sig {
-	case syscall.SIGTERM:
-		exit(0)
-	default:
-		exit(1)
+// NewTSOServiceCommand returns the unsafe remove failed stores command.
+func NewTSOServiceCommand() *cobra.Command {
+	cmd := &cobra.Command{
+		Use:   "tso",
+		Short: "Run the tso service",
+		Run:   tso.CreateServerWrapper,
 	}
+	cmd.Flags().BoolP("version", "V", false, "print version information and exit")
+	cmd.Flags().StringP("config", "", "", "config file")
+	cmd.Flags().StringP("backend-endpoints", "", "http://127.0.0.1:2379", "url for etcd client")
+	cmd.Flags().StringP("listen-addr", "", "", "listen address for tso service")
+	cmd.Flags().StringP("cacert", "", "", "path of file that contains list of trusted TLS CAs")
+	cmd.Flags().StringP("cert", "", "", "path of file that contains X509 certificate in PEM format")
+	cmd.Flags().StringP("key", "", "", "path of file that contains X509 key in PEM format")
+	return cmd
 }
 
-func createServerWrapper(args []string) (context.Context, context.CancelFunc, bs.Server) {
+func createServerWrapper(cmd *cobra.Command, args []string) {
 	schedulers.Register()
 	cfg := config.NewConfig()
-	err := cfg.Parse(args)
+	flagSet := cmd.Flags()
+	flagSet.Parse(args)
+	err := cfg.Parse(flagSet)
+	if err != nil {
+		cmd.Println(err)
+		return
+	}
 
-	if cfg.Version {
+	printVersion, err := flagSet.GetBool("version")
+	if err != nil {
+		cmd.Println(err)
+		return
+	}
+	if printVersion {
 		server.PrintPDInfo()
 		exit(0)
 	}
@@ -92,15 +133,21 @@ func createServerWrapper(args []string) (context.Context, context.CancelFunc, bs
 		log.Fatal("parse cmd flags error", errs.ZapError(err))
 	}
 
-	if cfg.ConfigCheck {
+	configCheck, err := flagSet.GetBool("config-check")
+	if err != nil {
+		cmd.Println(err)
+		return
+	}
+
+	if configCheck {
 		server.PrintConfigCheckMsg(cfg)
 		exit(0)
 	}
 
 	// New zap logger
-	err = cfg.SetupLogger()
+	err = logutil.SetupLogger(cfg.Log, &cfg.Logger, &cfg.LogProps, cfg.Security.RedactInfoLog)
 	if err == nil {
-		log.ReplaceGlobals(cfg.GetZapLogger(), cfg.GetZapLogProperties())
+		log.ReplaceGlobals(cfg.Logger, cfg.LogProps)
 	} else {
 		log.Fatal("initialize logger error", errs.ZapError(err))
 	}
@@ -132,7 +179,33 @@ func createServerWrapper(args []string) (context.Context, context.CancelFunc, bs
 		log.Fatal("create server failed", errs.ZapError(err))
 	}
 
-	return ctx, cancel, svr
+	sc := make(chan os.Signal, 1)
+	signal.Notify(sc,
+		syscall.SIGHUP,
+		syscall.SIGINT,
+		syscall.SIGTERM,
+		syscall.SIGQUIT)
+
+	var sig os.Signal
+	go func() {
+		sig = <-sc
+		cancel()
+	}()
+
+	if err := svr.Run(); err != nil {
+		log.Fatal("run server failed", errs.ZapError(err))
+	}
+
+	<-ctx.Done()
+	log.Info("Got signal to exit", zap.String("signal", sig.String()))
+
+	svr.Close()
+	switch sig {
+	case syscall.SIGTERM:
+		exit(0)
+	default:
+		exit(1)
+	}
 }
 
 func exit(code int) {
diff --git a/pkg/mcs/tso/server/server.go b/pkg/mcs/tso/server/server.go
index 4d336a4ef5b..29a7642591b 100644
--- a/pkg/mcs/tso/server/server.go
+++ b/pkg/mcs/tso/server/server.go
@@ -19,16 +19,19 @@ import (
 	"flag"
 	"net/http"
 	"os"
+	"os/signal"
+	"syscall"
 
 	grpcprometheus "github.com/grpc-ecosystem/go-grpc-prometheus"
 	"github.com/pingcap/errors"
 	"github.com/pingcap/log"
-	bs "github.com/tikv/pd/pkg/basicserver"
+	"github.com/spf13/cobra"
 	"github.com/tikv/pd/pkg/errs"
 	"github.com/tikv/pd/pkg/tso"
 	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/pkg/utils/metricutil"
 	"go.etcd.io/etcd/clientv3"
+	"go.uber.org/zap"
 )
 
 // Server is the TSO server, and it implements bs.Server.
@@ -69,12 +72,24 @@ func (s *Server) GetHTTPClient() *http.Client {
 }
 
 // CreateServerWrapper encapsulates the configuration/log/metrics initialization and create the server
-func CreateServerWrapper(args []string) (context.Context, context.CancelFunc, bs.Server) {
+func CreateServerWrapper(cmd *cobra.Command, args []string) {
+	cmd.Flags().Parse(args)
 	cfg := tso.NewConfig()
-	err := cfg.Parse(os.Args[1:])
+	flagSet := cmd.Flags()
+	err := cfg.Parse(flagSet)
+	if err != nil {
+		cmd.Println(err)
+		return
+	}
 
-	if cfg.Version {
-		printVersionInfo()
+	printVersion, err := flagSet.GetBool("version")
+	if err != nil {
+		cmd.Println(err)
+		return
+	}
+	if printVersion {
+		// TODO: support printing TSO server info
+		// server.PrintTSOInfo()
 		exit(0)
 	}
 
@@ -88,12 +103,18 @@ func CreateServerWrapper(args []string) (context.Context, context.CancelFunc, bs
 		log.Fatal("parse cmd flags error", errs.ZapError(err))
 	}
 
-	if cfg.ConfigCheck {
-		printConfigCheckMsg(cfg)
-		exit(0)
+	// New zap logger
+	err = logutil.SetupLogger(cfg.Log, &cfg.Logger, &cfg.LogProps, cfg.Security.RedactInfoLog)
+	if err == nil {
+		log.ReplaceGlobals(cfg.Logger, cfg.LogProps)
+	} else {
+		log.Fatal("initialize logger error", errs.ZapError(err))
 	}
+	// Flushing any buffered log entries
+	defer log.Sync()
 
-	// TODO: Initialize logger
+	// TODO: support printing TSO server info
+	// LogTSOInfo()
 
 	// TODO: Make it configurable if it has big impact on performance.
 	grpcprometheus.EnableHandlingTimeHistogram()
@@ -101,16 +122,36 @@ func CreateServerWrapper(args []string) (context.Context, context.CancelFunc, bs
 	metricutil.Push(&cfg.Metric)
 
 	// TODO: Create the server
+	ctx, cancel := context.WithCancel(context.Background())
+	svr := &Server{}
+
+	sc := make(chan os.Signal, 1)
+	signal.Notify(sc,
+		syscall.SIGHUP,
+		syscall.SIGINT,
+		syscall.SIGTERM,
+		syscall.SIGQUIT)
+
+	var sig os.Signal
+	go func() {
+		sig = <-sc
+		cancel()
+	}()
+
+	if err := svr.Run(); err != nil {
+		log.Fatal("run server failed", errs.ZapError(err))
+	}
 
-	return nil, nil, nil
-}
-
-// TODO: implement it
-func printVersionInfo() {
-}
+	<-ctx.Done()
+	log.Info("Got signal to exit", zap.String("signal", sig.String()))
 
-// TODO: implement it
-func printConfigCheckMsg(cfg *tso.Config) {
+	svr.Close()
+	switch sig {
+	case syscall.SIGTERM:
+		exit(0)
+	default:
+		exit(1)
+	}
 }
 
 func exit(code int) {
diff --git a/pkg/tso/config.go b/pkg/tso/config.go
index baf1fdc0062..9c20abbf307 100644
--- a/pkg/tso/config.go
+++ b/pkg/tso/config.go
@@ -15,12 +15,17 @@
 package tso
 
 import (
-	"flag"
 	"time"
 
+	"github.com/BurntSushi/toml"
 	"github.com/pingcap/errors"
+	"github.com/pingcap/log"
+	"github.com/spf13/pflag"
+	"github.com/tikv/pd/pkg/encryption"
+	"github.com/tikv/pd/pkg/utils/grpcutil"
 	"github.com/tikv/pd/pkg/utils/metricutil"
 	"github.com/tikv/pd/pkg/utils/typeutil"
+	"go.uber.org/zap"
 )
 
 const (
@@ -30,12 +35,8 @@ const (
 
 // Config is the configuration for the TSO.
 type Config struct {
-	flagSet *flag.FlagSet
-
-	Version bool `json:"-"`
-
-	ConfigCheck bool `json:"-"`
-	configFile  string
+	BackendEndpoints string `toml:"backend-endpoints" json:"backend-endpoints"`
+	ListenAddr       string `toml:"listen-addr" json:"listen-addr"`
 
 	// EnableLocalTSO is used to enable the Local TSO Allocator feature,
 	// which allows the PD server to generate Local TSO for certain DC-level transactions.
@@ -57,28 +58,61 @@ type Config struct {
 	MaxResetTSGap typeutil.Duration `toml:"max-gap-reset-ts" json:"max-gap-reset-ts"`
 
 	Metric metricutil.MetricConfig `toml:"metric" json:"metric"`
+
+	// Log related config.
+	Log log.Config `toml:"log" json:"log"`
+
+	Logger   *zap.Logger
+	LogProps *log.ZapProperties
+
+	Security SecurityConfig `toml:"security" json:"security"`
 }
 
 // NewConfig creates a new config.
 func NewConfig() *Config {
-	cfg := &Config{}
-	cfg.flagSet = flag.NewFlagSet("pd", flag.ContinueOnError)
-	fs := cfg.flagSet
-
-	fs.StringVar(&cfg.configFile, "config", "", "config file")
-
-	return cfg
+	return &Config{}
 }
 
 // Parse parses flag definitions from the argument list.
-func (c *Config) Parse(arguments []string) error {
-	// Parse first to get config file.
-	err := c.flagSet.Parse(arguments)
-	if err != nil {
-		return errors.WithStack(err)
+func (c *Config) Parse(flagSet *pflag.FlagSet) error {
+	// Load config file if specified.
+	if configFile, _ := flagSet.GetString("config"); configFile != "" {
+		_, err := c.configFromFile(configFile)
+		if err != nil {
+			return err
+		}
 	}
 
-	// TODO: Implement the main function body
+	// ignore the error check here
+	adjustCommandlineString(flagSet, &c.Log.Level, "log-level")
+	adjustCommandlineString(flagSet, &c.Log.File.Filename, "log-file")
+	adjustCommandlineString(flagSet, &c.Metric.PushAddress, "metrics-addr")
+	adjustCommandlineString(flagSet, &c.Security.CAPath, "cacert")
+	adjustCommandlineString(flagSet, &c.Security.CertPath, "cert")
+	adjustCommandlineString(flagSet, &c.Security.KeyPath, "key")
+	adjustCommandlineString(flagSet, &c.BackendEndpoints, "backend-endpoints")
+	adjustCommandlineString(flagSet, &c.ListenAddr, "listen-addr")
 
+	// TODO: Implement the main function body
 	return nil
 }
+
+// configFromFile loads config from file.
+func (c *Config) configFromFile(path string) (*toml.MetaData, error) {
+	meta, err := toml.DecodeFile(path, c)
+	return &meta, errors.WithStack(err)
+}
+
+// SecurityConfig indicates the security configuration for pd server
+type SecurityConfig struct {
+	grpcutil.TLSConfig
+	// RedactInfoLog indicates that whether enabling redact log
+	RedactInfoLog bool              `toml:"redact-info-log" json:"redact-info-log"`
+	Encryption    encryption.Config `toml:"encryption" json:"encryption"`
+}
+
+func adjustCommandlineString(flagSet *pflag.FlagSet, v *string, name string) {
+	if value, _ := flagSet.GetString(name); value != "" {
+		*v = value
+	}
+}
diff --git a/pkg/utils/logutil/log.go b/pkg/utils/logutil/log.go
index d98b9bc2e6c..a46f47da891 100644
--- a/pkg/utils/logutil/log.go
+++ b/pkg/utils/logutil/log.go
@@ -20,6 +20,7 @@ import (
 	"sync/atomic"
 
 	"github.com/pingcap/log"
+	"github.com/tikv/pd/pkg/errs"
 	"go.uber.org/zap"
 	"go.uber.org/zap/zapcore"
 )
@@ -65,6 +66,20 @@ func StringToZapLogLevel(level string) zapcore.Level {
 	return zapcore.InfoLevel
 }
 
+// SetupLogger setup the logger.
+func SetupLogger(logConfig log.Config, logger **zap.Logger, logProps **log.ZapProperties, enabled ...bool) error {
+	lg, p, err := log.InitLogger(&logConfig, zap.AddStacktrace(zapcore.FatalLevel))
+	if err != nil {
+		return errs.ErrInitLogger.Wrap(err).FastGenWithCause()
+	}
+	*logger = lg
+	*logProps = p
+	if len(enabled) > 0 {
+		SetRedactLog(enabled[0])
+	}
+	return nil
+}
+
 // LogPanic logs the panic reason and stack, then exit the process.
 // Commonly used with a `defer`.
 func LogPanic() {
diff --git a/server/api/server_test.go b/server/api/server_test.go
index 437f8c4888f..ed045e7de5e 100644
--- a/server/api/server_test.go
+++ b/server/api/server_test.go
@@ -28,6 +28,7 @@ import (
 	"github.com/stretchr/testify/suite"
 	"github.com/tikv/pd/pkg/utils/apiutil"
 	"github.com/tikv/pd/pkg/utils/assertutil"
+	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/pkg/utils/testutil"
 	"github.com/tikv/pd/server"
 	"github.com/tikv/pd/server/config"
@@ -84,10 +85,10 @@ func mustNewCluster(re *require.Assertions, num int, opts ...func(cfg *config.Co
 	ch := make(chan *server.Server, num)
 	for _, cfg := range cfgs {
 		go func(cfg *config.Config) {
-			err := cfg.SetupLogger()
+			err := logutil.SetupLogger(cfg.Log, &cfg.Logger, &cfg.LogProps, cfg.Security.RedactInfoLog)
 			re.NoError(err)
 			zapLogOnce.Do(func() {
-				log.ReplaceGlobals(cfg.GetZapLogger(), cfg.GetZapLogProperties())
+				log.ReplaceGlobals(cfg.Logger, cfg.LogProps)
 			})
 			for _, opt := range opts {
 				opt(cfg)
diff --git a/server/config/config.go b/server/config/config.go
index d5f39170932..ae1e27bfd22 100644
--- a/server/config/config.go
+++ b/server/config/config.go
@@ -17,7 +17,6 @@ package config
 import (
 	"crypto/tls"
 	"encoding/json"
-	"flag"
 	"fmt"
 	"math"
 	"net/url"
@@ -27,12 +26,12 @@ import (
 	"time"
 
 	"github.com/docker/go-units"
+	"github.com/spf13/pflag"
 	"github.com/tikv/pd/pkg/core/storelimit"
 	"github.com/tikv/pd/pkg/encryption"
 	"github.com/tikv/pd/pkg/errs"
 	"github.com/tikv/pd/pkg/utils/configutil"
 	"github.com/tikv/pd/pkg/utils/grpcutil"
-	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/pkg/utils/metricutil"
 	"github.com/tikv/pd/pkg/utils/syncutil"
 	"github.com/tikv/pd/pkg/utils/typeutil"
@@ -46,18 +45,11 @@ import (
 	"go.etcd.io/etcd/embed"
 	"go.etcd.io/etcd/pkg/transport"
 	"go.uber.org/zap"
-	"go.uber.org/zap/zapcore"
 )
 
 // Config is the pd server configuration.
 // NOTE: This type is exported by HTTP API. Please pay more attention when modifying it.
 type Config struct {
-	flagSet *flag.FlagSet
-
-	Version bool `json:"-"`
-
-	ConfigCheck bool `json:"-"`
-
 	ClientUrls          string `toml:"client-urls" json:"client-urls"`
 	PeerUrls            string `toml:"peer-urls" json:"peer-urls"`
 	AdvertiseClientUrls string `toml:"advertise-client-urls" json:"advertise-client-urls"`
@@ -150,8 +142,6 @@ type Config struct {
 
 	LabelProperty LabelPropertyConfig `toml:"label-property" json:"label-property"`
 
-	configFile string
-
 	// For all warnings during parsing.
 	WarningMsgs []string
 
@@ -160,8 +150,8 @@ type Config struct {
 	HeartbeatStreamBindInterval typeutil.Duration
 	LeaderPriorityCheckInterval typeutil.Duration
 
-	logger   *zap.Logger
-	logProps *log.ZapProperties
+	Logger   *zap.Logger        `json:"-"`
+	LogProps *log.ZapProperties `json:"-"`
 
 	Dashboard DashboardConfig `toml:"dashboard" json:"dashboard"`
 
@@ -172,36 +162,7 @@ type Config struct {
 
 // NewConfig creates a new config.
 func NewConfig() *Config {
-	cfg := &Config{}
-	cfg.flagSet = flag.NewFlagSet("pd", flag.ContinueOnError)
-	fs := cfg.flagSet
-
-	fs.BoolVar(&cfg.Version, "V", false, "print version information and exit")
-	fs.BoolVar(&cfg.Version, "version", false, "print version information and exit")
-	fs.StringVar(&cfg.configFile, "config", "", "config file")
-	fs.BoolVar(&cfg.ConfigCheck, "config-check", false, "check config file validity and exit")
-
-	fs.StringVar(&cfg.Name, "name", "", "human-readable name for this pd member")
-
-	fs.StringVar(&cfg.DataDir, "data-dir", "", "path to the data directory (default 'default.${name}')")
-	fs.StringVar(&cfg.ClientUrls, "client-urls", defaultClientUrls, "url for client traffic")
-	fs.StringVar(&cfg.AdvertiseClientUrls, "advertise-client-urls", "", "advertise url for client traffic (default '${client-urls}')")
-	fs.StringVar(&cfg.PeerUrls, "peer-urls", defaultPeerUrls, "url for peer traffic")
-	fs.StringVar(&cfg.AdvertisePeerUrls, "advertise-peer-urls", "", "advertise url for peer traffic (default '${peer-urls}')")
-	fs.StringVar(&cfg.InitialCluster, "initial-cluster", "", "initial cluster configuration for bootstrapping, e,g. pd=http://127.0.0.1:2380")
-	fs.StringVar(&cfg.Join, "join", "", "join to an existing cluster (usage: cluster's '${advertise-client-urls}'")
-
-	fs.StringVar(&cfg.Metric.PushAddress, "metrics-addr", "", "prometheus pushgateway address, leaves it empty will disable prometheus push")
-
-	fs.StringVar(&cfg.Log.Level, "L", "info", "log level: debug, info, warn, error, fatal (default 'info')")
-	fs.StringVar(&cfg.Log.File.Filename, "log-file", "", "log file path")
-
-	fs.StringVar(&cfg.Security.CAPath, "cacert", "", "path of file that contains list of trusted TLS CAs")
-	fs.StringVar(&cfg.Security.CertPath, "cert", "", "path of file that contains X509 certificate in PEM format")
-	fs.StringVar(&cfg.Security.KeyPath, "key", "", "path of file that contains X509 key in PEM format")
-	fs.BoolVar(&cfg.ForceNewCluster, "force-new-cluster", false, "force to create a new one-member cluster")
-
-	return cfg
+	return &Config{}
 }
 
 const (
@@ -391,54 +352,66 @@ func adjustPath(p *string) {
 }
 
 // Parse parses flag definitions from the argument list.
-func (c *Config) Parse(arguments []string) error {
-	// Parse first to get config file.
-	err := c.flagSet.Parse(arguments)
-	if err != nil {
-		return errors.WithStack(err)
-	}
-
+func (c *Config) Parse(flagSet *pflag.FlagSet) error {
 	// Load config file if specified.
 	var meta *toml.MetaData
-	if c.configFile != "" {
-		meta, err = c.configFromFile(c.configFile)
+	if configFile, _ := flagSet.GetString("config"); configFile != "" {
+		meta, err := c.configFromFile(configFile)
 		if err != nil {
 			return err
 		}
 
 		// Backward compatibility for toml config
 		if c.LogFileDeprecated != "" {
-			msg := fmt.Sprintf("log-file in %s is deprecated, use [log.file] instead", c.configFile)
+			msg := fmt.Sprintf("log-file in %s is deprecated, use [log.file] instead", configFile)
 			c.WarningMsgs = append(c.WarningMsgs, msg)
 			if c.Log.File.Filename == "" {
 				c.Log.File.Filename = c.LogFileDeprecated
 			}
 		}
 		if c.LogLevelDeprecated != "" {
-			msg := fmt.Sprintf("log-level in %s is deprecated, use [log] instead", c.configFile)
+			msg := fmt.Sprintf("log-level in %s is deprecated, use [log] instead", configFile)
 			c.WarningMsgs = append(c.WarningMsgs, msg)
 			if c.Log.Level == "" {
 				c.Log.Level = c.LogLevelDeprecated
 			}
 		}
 		if meta.IsDefined("schedule", "disable-raft-learner") {
-			msg := fmt.Sprintf("disable-raft-learner in %s is deprecated", c.configFile)
+			msg := fmt.Sprintf("disable-raft-learner in %s is deprecated", configFile)
 			c.WarningMsgs = append(c.WarningMsgs, msg)
 		}
 	}
 
-	// Parse again to replace with command line options.
-	err = c.flagSet.Parse(arguments)
-	if err != nil {
-		return errors.WithStack(err)
-	}
+	// ignore the error check here
+	adjustCommandlineString(flagSet, &c.Log.Level, "log-level")
+	adjustCommandlineString(flagSet, &c.Log.File.Filename, "log-file")
+	adjustCommandlineString(flagSet, &c.Name, "name")
+	adjustCommandlineString(flagSet, &c.DataDir, "data-dir")
+	adjustCommandlineString(flagSet, &c.ClientUrls, "client-urls")
+	adjustCommandlineString(flagSet, &c.AdvertiseClientUrls, "advertise-client-urls")
+	adjustCommandlineString(flagSet, &c.PeerUrls, "peer-urls")
+	adjustCommandlineString(flagSet, &c.AdvertisePeerUrls, "advertise-peer-urls")
+	adjustCommandlineString(flagSet, &c.InitialCluster, "initial-cluster")
+	adjustCommandlineString(flagSet, &c.Join, "join")
+	adjustCommandlineString(flagSet, &c.Metric.PushAddress, "metrics-addr")
+	adjustCommandlineString(flagSet, &c.Security.CAPath, "cacert")
+	adjustCommandlineString(flagSet, &c.Security.CertPath, "cert")
+	adjustCommandlineString(flagSet, &c.Security.KeyPath, "key")
+	adjustCommandlineBool(flagSet, &c.ForceNewCluster, "force-new-cluster")
+
+	return c.Adjust(meta, false)
+}
 
-	if len(c.flagSet.Args()) != 0 {
-		return errors.Errorf("'%s' is an invalid flag", c.flagSet.Arg(0))
+func adjustCommandlineString(flagSet *pflag.FlagSet, v *string, name string) {
+	if value, _ := flagSet.GetString(name); value != "" {
+		*v = value
 	}
+}
 
-	err = c.Adjust(meta, false)
-	return err
+func adjustCommandlineBool(flagSet *pflag.FlagSet, v *bool, name string) {
+	if value, _ := flagSet.GetBool(name); value {
+		*v = value
+	}
 }
 
 // Validate is used to validate if some configurations are right.
@@ -1301,33 +1274,6 @@ func (c LabelPropertyConfig) Clone() LabelPropertyConfig {
 	return m
 }
 
-// SetupLogger setup the logger.
-func (c *Config) SetupLogger() error {
-	lg, p, err := log.InitLogger(&c.Log, zap.AddStacktrace(zapcore.FatalLevel))
-	if err != nil {
-		return errs.ErrInitLogger.Wrap(err).FastGenWithCause()
-	}
-	c.logger = lg
-	c.logProps = p
-	logutil.SetRedactLog(c.Security.RedactInfoLog)
-	return nil
-}
-
-// GetZapLogger gets the created zap logger.
-func (c *Config) GetZapLogger() *zap.Logger {
-	return c.logger
-}
-
-// GetZapLogProperties gets properties of the zap logger.
-func (c *Config) GetZapLogProperties() *log.ZapProperties {
-	return c.logProps
-}
-
-// GetConfigFile gets the config file.
-func (c *Config) GetConfigFile() string {
-	return c.configFile
-}
-
 // IsLocalTSOEnabled returns if the local TSO is enabled.
 func (c *Config) IsLocalTSOEnabled() bool {
 	return c.EnableLocalTSO
@@ -1382,7 +1328,7 @@ func (c *Config) GenEmbedEtcdConfig() (*embed.Config, error) {
 	cfg.PeerTLSInfo.KeyFile = c.Security.KeyPath
 	cfg.PeerTLSInfo.AllowedCN = allowedCN
 	cfg.ForceNewCluster = c.ForceNewCluster
-	cfg.ZapLoggerBuilder = embed.NewZapCoreLoggerBuilder(c.logger, c.logger.Core(), c.logProps.Syncer)
+	cfg.ZapLoggerBuilder = embed.NewZapCoreLoggerBuilder(c.Logger, c.Logger.Core(), c.LogProps.Syncer)
 	cfg.EnableGRPCGateway = c.EnableGRPCGateway
 	cfg.EnableV2 = true
 	cfg.Logger = "zap"
diff --git a/server/config/config_test.go b/server/config/config_test.go
index a767b71a443..ee6c9e22287 100644
--- a/server/config/config_test.go
+++ b/server/config/config_test.go
@@ -24,6 +24,7 @@ import (
 	"time"
 
 	"github.com/BurntSushi/toml"
+	"github.com/spf13/pflag"
 	"github.com/stretchr/testify/require"
 	"github.com/tikv/pd/pkg/storage"
 	"github.com/tikv/pd/pkg/utils/configutil"
@@ -177,7 +178,13 @@ max-merge-region-size = 0
 enable-one-way-merge = true
 leader-schedule-limit = 0
 `
+
+	flagSet := pflag.NewFlagSet("test", pflag.ContinueOnError)
+	flagSet.StringP("log-level", "L", "info", "log level: debug, info, warn, error, fatal (default 'info')")
+	flagSet.Parse(nil)
 	cfg := NewConfig()
+	err := cfg.Parse(flagSet)
+	re.NoError(err)
 	meta, err := toml.Decode(cfgData, &cfg)
 	re.NoError(err)
 	err = cfg.Adjust(&meta, false)
diff --git a/server/server.go b/server/server.go
index 91e3e19ffda..3830fd574af 100644
--- a/server/server.go
+++ b/server/server.go
@@ -248,8 +248,8 @@ func CreateServer(ctx context.Context, cfg *config.Config, legacyServiceBuilders
 	}
 
 	s.etcdCfg = etcdCfg
-	s.lg = cfg.GetZapLogger()
-	s.logProps = cfg.GetZapLogProperties()
+	s.lg = cfg.Logger
+	s.logProps = cfg.LogProps
 	return s, nil
 }
 
diff --git a/server/testutil.go b/server/testutil.go
index 3820962ece3..05d68dce8e6 100644
--- a/server/testutil.go
+++ b/server/testutil.go
@@ -27,6 +27,7 @@ import (
 	"github.com/stretchr/testify/require"
 	"github.com/tikv/pd/pkg/utils/apiutil"
 	"github.com/tikv/pd/pkg/utils/assertutil"
+	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/pkg/utils/tempurl"
 	"github.com/tikv/pd/pkg/utils/testutil"
 	"github.com/tikv/pd/pkg/utils/typeutil"
@@ -86,10 +87,10 @@ func NewTestSingleConfig(c *assertutil.Checker) *config.Config {
 	cfg.TickInterval = typeutil.NewDuration(100 * time.Millisecond)
 	cfg.ElectionInterval = typeutil.NewDuration(3 * time.Second)
 	cfg.LeaderPriorityCheckInterval = typeutil.NewDuration(100 * time.Millisecond)
-	err := cfg.SetupLogger()
+	err := logutil.SetupLogger(cfg.Log, &cfg.Logger, &cfg.LogProps, cfg.Security.RedactInfoLog)
 	c.AssertNil(err)
 	zapLogOnce.Do(func() {
-		log.ReplaceGlobals(cfg.GetZapLogger(), cfg.GetZapLogProperties())
+		log.ReplaceGlobals(cfg.Logger, cfg.LogProps)
 	})
 
 	c.AssertNil(cfg.Adjust(nil, false))
diff --git a/tests/cluster.go b/tests/cluster.go
index e9fa55bcc24..ba1d619070e 100644
--- a/tests/cluster.go
+++ b/tests/cluster.go
@@ -34,6 +34,7 @@ import (
 	"github.com/tikv/pd/pkg/id"
 	"github.com/tikv/pd/pkg/swaggerserver"
 	"github.com/tikv/pd/pkg/tso"
+	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/pkg/utils/testutil"
 	"github.com/tikv/pd/server"
 	"github.com/tikv/pd/server/api"
@@ -73,12 +74,12 @@ var zapLogOnce sync.Once
 
 // NewTestServer creates a new TestServer.
 func NewTestServer(ctx context.Context, cfg *config.Config) (*TestServer, error) {
-	err := cfg.SetupLogger()
+	err := logutil.SetupLogger(cfg.Log, &cfg.Logger, &cfg.LogProps, cfg.Security.RedactInfoLog)
 	if err != nil {
 		return nil, err
 	}
 	zapLogOnce.Do(func() {
-		log.ReplaceGlobals(cfg.GetZapLogger(), cfg.GetZapLogProperties())
+		log.ReplaceGlobals(cfg.Logger, cfg.LogProps)
 	})
 	err = join.PrepareJoinCluster(cfg)
 	if err != nil {
diff --git a/tests/config.go b/tests/config.go
index 0c23d198184..4f653a3dc3c 100644
--- a/tests/config.go
+++ b/tests/config.go
@@ -19,6 +19,7 @@ import (
 	"os"
 	"strings"
 
+	"github.com/spf13/pflag"
 	"github.com/tikv/pd/pkg/utils/tempurl"
 	"github.com/tikv/pd/server/config"
 )
@@ -61,8 +62,31 @@ func (c *serverConfig) Generate(opts ...ConfigOption) (*config.Config, error) {
 		arguments = append(arguments, "--initial-cluster="+c.ClusterConfig.GetServerAddrs())
 	}
 
+	flagSet := pflag.NewFlagSet("test", pflag.ContinueOnError)
+	flagSet.BoolP("version", "V", false, "print version information and exit")
+	flagSet.StringP("config", "", "", "config file")
+	flagSet.BoolP("config-check", "", false, "check config file validity and exit")
+	flagSet.StringP("name", "", "", "human-readable name for this pd member")
+	flagSet.StringP("data-dir", "", "", "path to the data directory (default 'default.${name}')")
+	flagSet.StringP("client-urls", "", "http://127.0.0.1:2379", "url for client traffic")
+	flagSet.StringP("advertise-client-urls", "", "", "advertise url for client traffic (default '${client-urls}')")
+	flagSet.StringP("peer-urls", "", "http://127.0.0.1:2379", "url for peer traffic")
+	flagSet.StringP("advertise-peer-urls", "", "", "advertise url for peer traffic (default '${peer-urls}')")
+	flagSet.StringP("initial-cluster", "", "", "initial cluster configuration for bootstrapping, e,g. pd=http://127.0.0.1:2380")
+	flagSet.StringP("join", "", "", "join to an existing cluster (usage: cluster's '${advertise-client-urls}'")
+	flagSet.StringP("metrics-addr", "", "", "prometheus pushgateway address, leaves it empty will disable prometheus push")
+	flagSet.StringP("log-level", "L", "info", "log level: debug, info, warn, error, fatal (default 'info')")
+	flagSet.StringP("log-file", "", "", "log file path")
+	flagSet.StringP("cacert", "", "", "path of file that contains list of trusted TLS CAs")
+	flagSet.StringP("cert", "", "", "path of file that contains X509 certificate in PEM format")
+	flagSet.StringP("key", "", "", "path of file that contains X509 key in PEM format")
+	flagSet.BoolP("force-new-cluster", "", false, "force to create a new one-member cluster")
+	err := flagSet.Parse(arguments)
+	if err != nil {
+		return nil, err
+	}
 	cfg := config.NewConfig()
-	err := cfg.Parse(arguments)
+	err = cfg.Parse(flagSet)
 	if err != nil {
 		return nil, err
 	}
diff --git a/tools/pd-heartbeat-bench/config/config.go b/tools/pd-heartbeat-bench/config/config.go
index 5d59bb52974..d85e68bfb60 100644
--- a/tools/pd-heartbeat-bench/config/config.go
+++ b/tools/pd-heartbeat-bench/config/config.go
@@ -6,7 +6,6 @@ import (
 	"github.com/pingcap/log"
 	flag "github.com/spf13/pflag"
 	"go.uber.org/zap"
-	"go.uber.org/zap/zapcore"
 )
 
 const (
@@ -32,8 +31,8 @@ type Config struct {
 	StatusAddr string
 
 	Log      log.Config `toml:"log" json:"log"`
-	logger   *zap.Logger
-	logProps *log.ZapProperties
+	Logger   *zap.Logger
+	LogProps *log.ZapProperties
 
 	StoreCount        int     `toml:"store-count" json:"store-count"`
 	RegionCount       int     `toml:"region-count" json:"region-count"`
@@ -138,27 +137,6 @@ func (c *Config) configFromFile(path string) (*toml.MetaData, error) {
 	return &meta, err
 }
 
-// SetupLogger setup the logger.
-func (c *Config) SetupLogger() error {
-	lg, p, err := log.InitLogger(&c.Log, zap.AddStacktrace(zapcore.FatalLevel))
-	if err != nil {
-		return err
-	}
-	c.logger = lg
-	c.logProps = p
-	return nil
-}
-
-// GetZapLogger gets the created zap logger.
-func (c *Config) GetZapLogger() *zap.Logger {
-	return c.logger
-}
-
-// GetZapLogProperties gets properties of the zap logger.
-func (c *Config) GetZapLogProperties() *log.ZapProperties {
-	return c.logProps
-}
-
 func adjustFloat64(v *float64, defValue float64) {
 	if *v == 0 {
 		*v = defValue
diff --git a/tools/pd-heartbeat-bench/main.go b/tools/pd-heartbeat-bench/main.go
index 15d955c57ef..cec110cb635 100644
--- a/tools/pd-heartbeat-bench/main.go
+++ b/tools/pd-heartbeat-bench/main.go
@@ -408,9 +408,9 @@ func main() {
 	}
 
 	// New zap logger
-	err = cfg.SetupLogger()
+	err = logutil.SetupLogger(cfg.Log, &cfg.Logger, &cfg.LogProps)
 	if err == nil {
-		log.ReplaceGlobals(cfg.GetZapLogger(), cfg.GetZapLogProperties())
+		log.ReplaceGlobals(cfg.Logger, cfg.LogProps)
 	} else {
 		log.Fatal("initialize logger error", zap.Error(err))
 	}
diff --git a/tools/pd-simulator/main.go b/tools/pd-simulator/main.go
index c37f4502b99..8e646998714 100644
--- a/tools/pd-simulator/main.go
+++ b/tools/pd-simulator/main.go
@@ -28,6 +28,7 @@ import (
 	"github.com/pingcap/log"
 	"github.com/prometheus/client_golang/prometheus/promhttp"
 	flag "github.com/spf13/pflag"
+	"github.com/tikv/pd/pkg/utils/logutil"
 	"github.com/tikv/pd/server"
 	"github.com/tikv/pd/server/api"
 	"github.com/tikv/pd/server/config"
@@ -132,18 +133,13 @@ func runHTTPServer() {
 
 // NewSingleServer creates a pd server for simulator.
 func NewSingleServer(ctx context.Context, simConfig *simulator.SimConfig) (*server.Server, server.CleanupFunc) {
-	err := simConfig.ServerConfig.SetupLogger()
+	err := logutil.SetupLogger(simConfig.ServerConfig.Log, &simConfig.ServerConfig.Logger, &simConfig.ServerConfig.LogProps)
 	if err == nil {
-		log.ReplaceGlobals(simConfig.ServerConfig.GetZapLogger(), simConfig.ServerConfig.GetZapLogProperties())
+		log.ReplaceGlobals(simConfig.ServerConfig.Logger, simConfig.ServerConfig.LogProps)
 	} else {
 		log.Fatal("setup logger error", zap.Error(err))
 	}
 
-	simConfig.ServerConfig.SetupLogger()
-	if err != nil {
-		log.Fatal("initialize logger error", zap.Error(err))
-	}
-
 	s, err := server.CreateServer(ctx, simConfig.ServerConfig, api.NewHandler)
 	if err != nil {
 		panic("create server failed")