diff --git a/cdc/sink/mysql/mysql_syncpoint_store.go b/cdc/sink/mysql/mysql_syncpoint_store.go
index 5da5176fcb4..5e1d447911e 100644
--- a/cdc/sink/mysql/mysql_syncpoint_store.go
+++ b/cdc/sink/mysql/mysql_syncpoint_store.go
@@ -243,12 +243,14 @@ func (s *mysqlSyncPointStore) SinkSyncPoint(ctx context.Context,
 			s.syncPointRetention.Seconds())
 		_, err = tx.Exec(query)
 		if err != nil {
-			// It is ok to ignore the error, since it will not affect the correctness of the system,
-			// and no any business logic depends on this behavior, so we just log the error.
-			log.Error("failed to clean syncpoint table", zap.Error(cerror.WrapError(cerror.ErrMySQLTxnError, err)))
-		} else {
-			s.lastCleanSyncPointTime = time.Now()
+			err2 := tx.Rollback()
+			// It is ok to ignore the error, since clear sync point is not necessary.
+			if err2 != nil {
+				log.Error("failed to clean syncpoint table", zap.Error(cerror.WrapError(cerror.ErrMySQLTxnError, err2)))
+			}
 		}
+		s.lastCleanSyncPointTime = time.Now()
+		log.Info("clean outdate syncpoint successfully", zap.String("query", query))
 	}
 
 	err = tx.Commit()