diff --git a/internal/datacoord/meta.go b/internal/datacoord/meta.go
index f074323bc811..efa0ed55b999 100644
--- a/internal/datacoord/meta.go
+++ b/internal/datacoord/meta.go
@@ -519,14 +519,15 @@ func (m *meta) UpdateFlushSegmentsInfo(
 
 	if importing {
 		s := clonedSegment
+		s.NumOfRows = s.currRows
 		count := segmentutil.CalcRowCountFromBinLog(s.SegmentInfo)
-		if count != segment.currRows {
+		if count != segment.currRows && count > 0 {
 			log.Info("check point reported inconsistent with bin log row count",
 				zap.Int64("segment ID", segment.GetID()),
 				zap.Int64("current rows (wrong)", segment.currRows),
 				zap.Int64("segment bin log row count (correct)", count))
+			s.NumOfRows = count
 		}
-		s.NumOfRows = count
 		modSegments[segmentID] = s
 	} else {
 		for _, cp := range checkpoints {
@@ -543,15 +544,16 @@ func (m *meta) UpdateFlushSegmentsInfo(
 				continue
 			}
 
+			s.NumOfRows = cp.NumOfRows
 			count := segmentutil.CalcRowCountFromBinLog(s.SegmentInfo)
 			// count should smaller than or equal to cp reported
-			if count != cp.NumOfRows {
+			if count != cp.NumOfRows && count > 0 {
 				log.Info("check point reported inconsistent with bin log row count",
 					zap.Int64("segment ID", segment.GetID()),
 					zap.Int64("check point (wrong)", cp.NumOfRows),
 					zap.Int64("segment bin log row count (correct)", count))
+				s.NumOfRows = count
 			}
-			s.NumOfRows = count
 
 			s.DmlPosition = cp.GetPosition()
 			modSegments[cp.GetSegmentID()] = s
diff --git a/internal/datacoord/meta_test.go b/internal/datacoord/meta_test.go
index 98ddaeae7869..64c88e1bc0f6 100644
--- a/internal/datacoord/meta_test.go
+++ b/internal/datacoord/meta_test.go
@@ -384,7 +384,7 @@ func TestUpdateFlushSegmentsInfo(t *testing.T) {
 		err = meta.AddSegment(segment1)
 		assert.Nil(t, err)
 
-		err = meta.UpdateFlushSegmentsInfo(1, true, false, true, []*datapb.FieldBinlog{getFieldBinlogPathsWithEntry(1, 10, getInsertLogPath("binlog1", 1))},
+		err = meta.UpdateFlushSegmentsInfo(1, true, false, false, []*datapb.FieldBinlog{getFieldBinlogPathsWithEntry(1, 10, getInsertLogPath("binlog1", 1))},
 			[]*datapb.FieldBinlog{getFieldBinlogPaths(1, getStatsLogPath("statslog1", 1))},
 			[]*datapb.FieldBinlog{{Binlogs: []*datapb.Binlog{{EntriesNum: 1, TimestampFrom: 100, TimestampTo: 200, LogSize: 1000, LogPath: getDeltaLogPath("deltalog1", 1)}}}},
 			[]*datapb.CheckPoint{{SegmentID: 1, NumOfRows: 10}}, []*datapb.SegmentStartPosition{{SegmentID: 1, StartPosition: &internalpb.MsgPosition{MsgID: []byte{1, 2, 3}}}})
diff --git a/internal/datacoord/services.go b/internal/datacoord/services.go
index c01736f9827a..bcb2de6dc8d8 100644
--- a/internal/datacoord/services.go
+++ b/internal/datacoord/services.go
@@ -724,7 +724,7 @@ func (s *Server) GetRecoveryInfo(ctx context.Context, req *datapb.GetRecoveryInf
 			segment2Binlogs[id] = append(segment2Binlogs[id], fieldBinlogs)
 		}
 
-		if newCount := segmentutil.CalcRowCountFromBinLog(segment.SegmentInfo); newCount != segment.NumOfRows {
+		if newCount := segmentutil.CalcRowCountFromBinLog(segment.SegmentInfo); newCount != segment.NumOfRows && newCount > 0 {
 			log.Warn("segment row number meta inconsistent with bin log row count and will be corrected",
 				zap.Int64("segment ID", segment.GetID()),
 				zap.Int64("segment meta row count (wrong)", segment.GetNumOfRows()),
diff --git a/internal/util/segmentutil/utils.go b/internal/util/segmentutil/utils.go
index 07f3046dfafd..36ceeda269b4 100644
--- a/internal/util/segmentutil/utils.go
+++ b/internal/util/segmentutil/utils.go
@@ -11,7 +11,7 @@ import (
 // Note that `segCloned` should be a copied version of `seg`.
 func ReCalcRowCount(seg, segCloned *datapb.SegmentInfo) {
 	// `segment` is not mutated but only cloned above and is safe to be referred here.
-	if newCount := CalcRowCountFromBinLog(seg); newCount != seg.GetNumOfRows() {
+	if newCount := CalcRowCountFromBinLog(seg); newCount != seg.GetNumOfRows() && newCount > 0 {
 		log.Warn("segment row number meta inconsistent with bin log row count and will be corrected",
 			zap.Int64("segment ID", seg.GetID()),
 			zap.Int64("segment meta row count (wrong)", seg.GetNumOfRows()),
@@ -27,6 +27,10 @@ func CalcRowCountFromBinLog(seg *datapb.SegmentInfo) int64 {
 	if len(seg.GetBinlogs()) > 0 {
 		for _, ct := range seg.GetBinlogs()[0].GetBinlogs() {
 			rowCt += ct.GetEntriesNum()
+			// This segment contains stale log with incorrect entries num,
+			if ct.GetEntriesNum() <= 0 {
+				return -1
+			}
 		}
 	}
 	return rowCt