diff --git a/ddl/syncer/syncer.go b/ddl/syncer/syncer.go
index 3cdccb0197cc5..c7f13b68d2ead 100644
--- a/ddl/syncer/syncer.go
+++ b/ddl/syncer/syncer.go
@@ -337,13 +337,15 @@ func (s *schemaVersionSyncer) OwnerCheckAllVersions(ctx context.Context, jobID i
 		if variable.EnableMDL.Load() {
 			for _, kv := range resp.Kvs {
 				key := string(kv.Key)
+				tidbIDInResp := key[strings.LastIndex(key, "/")+1:]
 				ver, err := strconv.Atoi(string(kv.Value))
 				if err != nil {
 					logutil.BgLogger().Info("syncer check all versions, convert value to int failed, continue checking.", zap.String("category", "ddl"), zap.String("ddl", string(kv.Key)), zap.String("value", string(kv.Value)), zap.Error(err))
 					succ = false
 					break
 				}
-				if int64(ver) < latestVer {
+				// We need to check if the tidb ID is in the updatedMap, in case that deleting etcd is failed, and tidb server is down.
+				if int64(ver) < latestVer && updatedMap[tidbIDInResp] != "" {
 					if notMatchVerCnt%intervalCnt == 0 {
 						logutil.BgLogger().Info("syncer check all versions, someone is not synced, continue checking", zap.String("category", "ddl"),
 							zap.String("ddl", string(kv.Key)), zap.Int("currentVer", ver), zap.Int64("latestVer", latestVer))
@@ -352,7 +354,7 @@ func (s *schemaVersionSyncer) OwnerCheckAllVersions(ctx context.Context, jobID i
 					notMatchVerCnt++
 					break
 				}
-				delete(updatedMap, key[strings.LastIndex(key, "/")+1:])
+				delete(updatedMap, tidbIDInResp)
 			}
 			if len(updatedMap) > 0 {
 				succ = false