diff --git a/server/src/main/java/org/apache/iotdb/db/conf/IoTDBConfigCheck.java b/server/src/main/java/org/apache/iotdb/db/conf/IoTDBConfigCheck.java
index ffbba6eba3158..992ef36b2eca6 100644
--- a/server/src/main/java/org/apache/iotdb/db/conf/IoTDBConfigCheck.java
+++ b/server/src/main/java/org/apache/iotdb/db/conf/IoTDBConfigCheck.java
@@ -241,6 +241,14 @@ private void upgradePropertiesFile() throws IOException {
       System.exit(-1);
     }
 
+    // virtual storage group num can only set to 1 when upgrading from old version
+    if (!virtualStorageGroupNum.equals("1")) {
+      logger.error(
+          "virtual storage group num cannot set to {} when upgrading from old version, "
+              + "please set to 1 and restart",
+          virtualStorageGroupNum);
+      System.exit(-1);
+    }
     try (FileOutputStream tmpFOS = new FileOutputStream(tmpPropertiesFile.toString())) {
       properties.setProperty(PARTITION_INTERVAL_STRING, String.valueOf(partitionInterval));
       properties.setProperty(TSFILE_FILE_SYSTEM_STRING, tsfileFileSystem);
@@ -432,6 +440,16 @@ private void moveFileToUpgradeFolder(List<String> folders) {
         if (!storageGroup.isDirectory()) {
           continue;
         }
+        // create virtual storage group folder 0
+        File virtualStorageGroupDir = fsFactory.getFile(storageGroup, "0");
+        if (virtualStorageGroupDir.mkdirs()) {
+          logger.info(
+              "virtual storage directory {} doesn't exist, create it",
+              virtualStorageGroupDir.getPath());
+        } else if (!virtualStorageGroupDir.exists()) {
+          logger.error(
+              "Create virtual storage directory {} failed", virtualStorageGroupDir.getPath());
+        }
         for (File partitionDir : storageGroup.listFiles()) {
           if (!partitionDir.isDirectory()) {
             continue;
@@ -450,7 +468,8 @@ private void moveFileToUpgradeFolder(List<String> folders) {
           if (oldTsfileArray.length + oldResourceFileArray.length + oldModificationFileArray.length
               != 0) {
             // create upgrade directory if not exist
-            File upgradeFolder = fsFactory.getFile(partitionDir, IoTDBConstant.UPGRADE_FOLDER_NAME);
+            File upgradeFolder =
+                fsFactory.getFile(virtualStorageGroupDir, IoTDBConstant.UPGRADE_FOLDER_NAME);
             if (upgradeFolder.mkdirs()) {
               logger.info("Upgrade Directory {} doesn't exist, create it", upgradeFolder.getPath());
             } else if (!upgradeFolder.exists()) {
@@ -475,6 +494,13 @@ private void moveFileToUpgradeFolder(List<String> folders) {
               }
             }
           }
+          if (partitionDir.listFiles().length == 0) {
+            try {
+              Files.delete(partitionDir.toPath());
+            } catch (IOException e) {
+              logger.error("Delete {} failed", partitionDir);
+            }
+          }
         }
       }
     }
diff --git a/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/file/metadata/TsFileMetadataV2.java b/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/file/metadata/TsFileMetadataV2.java
index 9825a5c20c068..2ebd12e7a7099 100644
--- a/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/file/metadata/TsFileMetadataV2.java
+++ b/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/file/metadata/TsFileMetadataV2.java
@@ -24,6 +24,7 @@
 import org.apache.iotdb.tsfile.utils.ReadWriteIOUtils;
 
 import java.nio.ByteBuffer;
+import java.util.ArrayList;
 import java.util.List;
 
 public class TsFileMetadataV2 {
@@ -34,12 +35,12 @@ private TsFileMetadataV2() {}
    * deserialize data from the buffer.
    *
    * @param buffer -buffer use to deserialize
-   * @return -a instance of TsFileMetaData
+   * @return -a pair of TsFileMetaData and VersionInfo
    */
-  public static TsFileMetadata deserializeFrom(
-      ByteBuffer buffer, List<Pair<Long, Long>> versionInfo) {
+  public static Pair<TsFileMetadata, List<Pair<Long, Long>>> deserializeFrom(ByteBuffer buffer) {
     TsFileMetadata fileMetaData = new TsFileMetadata();
 
+    List<Pair<Long, Long>> versionInfo = new ArrayList<>();
     // metadataIndex
     fileMetaData.setMetadataIndex(MetadataIndexNodeV2.deserializeFrom(buffer));
     // totalChunkNum
@@ -70,6 +71,6 @@ public static TsFileMetadata deserializeFrom(
           BloomFilter.buildBloomFilter(bytes, filterSize, hashFunctionSize));
     }
 
-    return fileMetaData;
+    return new Pair<>(fileMetaData, versionInfo);
   }
 }
diff --git a/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/read/TsFileSequenceReaderForV2.java b/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/read/TsFileSequenceReaderForV2.java
index d07007b6d0cdd..117da82cfc775 100644
--- a/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/read/TsFileSequenceReaderForV2.java
+++ b/tsfile/src/main/java/org/apache/iotdb/tsfile/v2/read/TsFileSequenceReaderForV2.java
@@ -145,11 +145,11 @@ public String readVersionNumberV2() throws IOException {
    */
   @Override
   public TsFileMetadata readFileMetadata() throws IOException {
-    if (tsFileMetaData == null) {
-      versionInfo = new ArrayList<>();
-      tsFileMetaData =
-          TsFileMetadataV2.deserializeFrom(
-              readData(fileMetadataPos, fileMetadataSize), versionInfo);
+    if (tsFileMetaData == null || versionInfo == null) {
+      Pair<TsFileMetadata, List<Pair<Long, Long>>> pair =
+          TsFileMetadataV2.deserializeFrom(readData(fileMetadataPos, fileMetadataSize));
+      tsFileMetaData = pair.left;
+      versionInfo = pair.right;
     }
     return tsFileMetaData;
   }