diff --git a/pkg/bootstrap/versions/v2_0_1/pubsub.go b/pkg/bootstrap/versions/v2_0_1/pubsub.go
index 899d95fc63f13..f8def79d7dfb7 100644
--- a/pkg/bootstrap/versions/v2_0_1/pubsub.go
+++ b/pkg/bootstrap/versions/v2_0_1/pubsub.go
@@ -107,6 +107,11 @@ func migrateMoPubs(txn executor.TxnExecutor) (err error) {
 		if _, err = txn.Exec(insertSql, executor.StatementOption{}.WithAccountID(0)); err != nil {
 			return
 		}
+
+		deleteSql := fmt.Sprintf("delete from mo_catalog.mo_subs where pub_account_name = '%s' and pub_name = '%s' and sub_name is null", info.PubAccountName, info.PubName)
+		if _, err = txn.Exec(deleteSql, executor.StatementOption{}.WithAccountID(0)); err != nil {
+			return
+		}
 	}
 	return
 }
diff --git a/pkg/bootstrap/versions/v2_0_1/pubsub_test.go b/pkg/bootstrap/versions/v2_0_1/pubsub_test.go
index c9784c034fc4d..b568d99001a8f 100644
--- a/pkg/bootstrap/versions/v2_0_1/pubsub_test.go
+++ b/pkg/bootstrap/versions/v2_0_1/pubsub_test.go
@@ -15,6 +15,7 @@
 package v2_0_1
 
 import (
+	"strings"
 	"testing"
 
 	"github.com/matrixorigin/matrixone/pkg/bootstrap/versions"
@@ -27,7 +28,9 @@ import (
 	"github.com/stretchr/testify/assert"
 )
 
-type MockTxnExecutor struct{}
+type MockTxnExecutor struct {
+	flag bool
+}
 
 func (MockTxnExecutor) Use(db string) {
 	//TODO implement me
@@ -39,7 +42,11 @@ func (MockTxnExecutor) LockTable(table string) error {
 	panic("implement me")
 }
 
-func (MockTxnExecutor) Exec(sql string, options executor.StatementOption) (executor.Result, error) {
+func (e MockTxnExecutor) Exec(sql string, options executor.StatementOption) (executor.Result, error) {
+	if strings.HasPrefix(sql, "delete from mo_catalog.mo_subs") && e.flag {
+		return executor.Result{}, assert.AnError
+	}
+
 	bat := batch.New([]string{"a"})
 	bat.Vecs[0] = testutil.MakeInt32Vector([]int32{1}, nil)
 	bat.SetRowCount(1)
@@ -106,3 +113,46 @@ func Test_migrateMoPubs(t *testing.T) {
 	err := migrateMoPubs(txn)
 	assert.NoError(t, err)
 }
+
+func Test_migrateMoPubs_deleteFailed(t *testing.T) {
+	getAccountsStub := gostub.Stub(
+		&pubsub.GetAccounts,
+		func(_ executor.TxnExecutor) (map[string]*pubsub.AccountInfo, map[int32]*pubsub.AccountInfo, error) {
+			return map[string]*pubsub.AccountInfo{
+				"acc1": {Id: 1, Name: "acc1"},
+			}, nil, nil
+		},
+	)
+	defer getAccountsStub.Reset()
+
+	getAllPubInfosStub := gostub.Stub(
+		&versions.GetAllPubInfos,
+		func(_ executor.TxnExecutor, _ map[string]*pubsub.AccountInfo) (map[string]*pubsub.PubInfo, error) {
+			return map[string]*pubsub.PubInfo{
+				"sys#pubName": {
+					PubAccountName: "sys",
+					PubName:        "pubName",
+					SubAccountsStr: pubsub.AccountAll,
+				},
+				"acc1#pubName": {
+					PubAccountName: "acc1",
+					PubName:        "pubName",
+					SubAccountsStr: pubsub.AccountAll,
+				},
+			}, nil
+		},
+	)
+	defer getAllPubInfosStub.Reset()
+
+	getSubbedAccNamesStub := gostub.Stub(
+		&getSubbedAccNames,
+		func(_ executor.TxnExecutor, _, _ string, _ map[int32]*pubsub.AccountInfo) ([]string, error) {
+			return []string{"acc2"}, nil
+		},
+	)
+	defer getSubbedAccNamesStub.Reset()
+
+	txn := &MockTxnExecutor{flag: true}
+	err := migrateMoPubs(txn)
+	assert.Error(t, err)
+}