diff --git a/pkg/ddl/constant.go b/pkg/ddl/constant.go
index 212c84126814b..165172ebfe1a3 100644
--- a/pkg/ddl/constant.go
+++ b/pkg/ddl/constant.go
@@ -25,6 +25,8 @@ const (
 	ReorgTable = "tidb_ddl_reorg"
 	// HistoryTable stores the history DDL jobs.
 	HistoryTable = "tidb_ddl_history"
+	// MDLInfoTable stores lock info used by metadata lock.
+	MDLInfoTable = "tidb_mdl_info"
 
 	// JobTableID is the table ID of `tidb_ddl_job`.
 	JobTableID = meta.MaxInt48 - 1
diff --git a/pkg/ddl/ddl_worker.go b/pkg/ddl/ddl_worker.go
index 3e2c5a96cfd8f..ab755b3366561 100644
--- a/pkg/ddl/ddl_worker.go
+++ b/pkg/ddl/ddl_worker.go
@@ -20,6 +20,7 @@ import (
 	"math/rand"
 	"os"
 	"strconv"
+	"strings"
 	"sync"
 	"sync/atomic"
 	"time"
@@ -36,6 +37,7 @@ import (
 	"github.com/pingcap/tidb/pkg/parser"
 	"github.com/pingcap/tidb/pkg/parser/ast"
 	"github.com/pingcap/tidb/pkg/parser/model"
+	"github.com/pingcap/tidb/pkg/parser/mysql"
 	"github.com/pingcap/tidb/pkg/parser/terror"
 	"github.com/pingcap/tidb/pkg/sessionctx"
 	"github.com/pingcap/tidb/pkg/sessionctx/binloginfo"
@@ -590,6 +592,11 @@ func (w *worker) updateDDLJob(job *model.Job, meetErr bool) error {
 	return errors.Trace(updateDDLJob2Table(w.sess, job, updateRawArgs))
 }
 
+func matchMDLInfoTable(schemaName, tblName string) bool {
+	return strings.ToLower(schemaName) == mysql.SystemDB &&
+		strings.ToLower(tblName) == MDLInfoTable
+}
+
 // registerMDLInfo registers metadata lock info.
 func (w *worker) registerMDLInfo(job *model.Job, ver int64) error {
 	if !variable.EnableMDL.Load() {
@@ -607,31 +614,45 @@ func (w *worker) registerMDLInfo(job *model.Job, ver int64) error {
 	}
 	ownerID := w.ownerManager.ID()
 	ids := rows[0].GetString(0)
-	sql := fmt.Sprintf("replace into mysql.tidb_mdl_info (job_id, version, table_ids, owner_id) values (%d, %d, '%s', '%s')", job.ID, ver, ids, ownerID)
+	var sql string
+	if matchMDLInfoTable(job.SchemaName, job.TableName) {
+		// DDLs that modify system table `tidb_mdl_info` could only happen in upgrade process,
+		// we should not reference 'owner_id'. Otherwise, there is a circular problem.
+		sql = fmt.Sprintf("replace into mysql.tidb_mdl_info (job_id, version, table_ids) values (%d, %d, '%s')", job.ID, ver, ids)
+	} else {
+		sql = fmt.Sprintf("replace into mysql.tidb_mdl_info (job_id, version, table_ids, owner_id) values (%d, %d, '%s', '%s')", job.ID, ver, ids, ownerID)
+	}
 	_, err = w.sess.Execute(context.Background(), sql, "register-mdl-info")
 	return err
 }
 
 // cleanMDLInfo cleans metadata lock info.
-func cleanMDLInfo(pool *sess.Pool, jobID int64, ec *clientv3.Client, ownerID string, cleanETCD bool) {
+func cleanMDLInfo(pool *sess.Pool, job *model.Job, ec *clientv3.Client, ownerID string, cleanETCD bool) {
 	if !variable.EnableMDL.Load() {
 		return
 	}
-	sql := fmt.Sprintf("delete from mysql.tidb_mdl_info where job_id = %d and owner_id = '%s'", jobID, ownerID)
+	var sql string
+	if matchMDLInfoTable(job.SchemaName, job.TableName) {
+		// DDLs that modify system table `tidb_mdl_info` could only happen in upgrade process,
+		// we should not reference 'owner_id'. Otherwise, there is a circular problem.
+		sql = fmt.Sprintf("delete from mysql.tidb_mdl_info where job_id = %d", job.ID)
+	} else {
+		sql = fmt.Sprintf("delete from mysql.tidb_mdl_info where job_id = %d and owner_id = '%s'", job.ID, ownerID)
+	}
 	sctx, _ := pool.Get()
 	defer pool.Put(sctx)
 	se := sess.NewSession(sctx)
 	se.GetSessionVars().SetDiskFullOpt(kvrpcpb.DiskFullOpt_AllowedOnAlmostFull)
 	_, err := se.Execute(context.Background(), sql, "delete-mdl-info")
 	if err != nil {
-		logutil.DDLLogger().Warn("unexpected error when clean mdl info", zap.Int64("job ID", jobID), zap.Error(err))
+		logutil.DDLLogger().Warn("unexpected error when clean mdl info", zap.Int64("job ID", job.ID), zap.Error(err))
 		return
 	}
 	if cleanETCD && ec != nil {
-		path := fmt.Sprintf("%s/%d/", util.DDLAllSchemaVersionsByJob, jobID)
+		path := fmt.Sprintf("%s/%d/", util.DDLAllSchemaVersionsByJob, job.ID)
 		_, err = ec.Delete(context.Background(), path, clientv3.WithPrefix())
 		if err != nil {
-			logutil.DDLLogger().Warn("delete versions failed", zap.Int64("job ID", jobID), zap.Error(err))
+			logutil.DDLLogger().Warn("delete versions failed", zap.Int64("job ID", job.ID), zap.Error(err))
 		}
 	}
 }
diff --git a/pkg/ddl/job_table.go b/pkg/ddl/job_table.go
index 76dd37f98082d..59125be52b429 100644
--- a/pkg/ddl/job_table.go
+++ b/pkg/ddl/job_table.go
@@ -443,7 +443,7 @@ func (d *ddl) delivery2Worker(wk *worker, pool *workerPool, job *model.Job) {
 						return
 					}
 					d.setAlreadyRunOnce(job.ID)
-					cleanMDLInfo(d.sessPool, job.ID, d.etcdCli, ownerID, job.State == model.JobStateSynced)
+					cleanMDLInfo(d.sessPool, job, d.etcdCli, ownerID, job.State == model.JobStateSynced)
 					// Don't have a worker now.
 					return
 				}
@@ -481,7 +481,7 @@ func (d *ddl) delivery2Worker(wk *worker, pool *workerPool, job *model.Job) {
 			if err != nil {
 				return
 			}
-			cleanMDLInfo(d.sessPool, job.ID, d.etcdCli, ownerID, job.State == model.JobStateSynced)
+			cleanMDLInfo(d.sessPool, job, d.etcdCli, ownerID, job.State == model.JobStateSynced)
 			d.synced(job)
 
 			if RunInGoTest {