diff --git a/session/bootstrap.go b/session/bootstrap.go
index a3c98a014b4e2..104e01b230f8b 100644
--- a/session/bootstrap.go
+++ b/session/bootstrap.go
@@ -732,11 +732,13 @@ const (
 	version107 = 107
 	// version108 adds the table tidb_ttl_table_status
 	version108 = 108
+	// version109 sets tidb_enable_gc_aware_memory_track to off when a cluster upgrades from some version lower than v6.5.0.
+	version109 = 109
 )
 
 // currentBootstrapVersion is defined as a variable, so we can modify its value for testing.
 // please make sure this is the largest version
-var currentBootstrapVersion int64 = version108
+var currentBootstrapVersion int64 = version109
 
 // DDL owner key's expired time is ManagerSessionTTL seconds, we should wait the time and give more time to have a chance to finish it.
 var internalSQLTimeout = owner.ManagerSessionTTL + 15
@@ -849,6 +851,7 @@ var (
 		upgradeToVer106,
 		upgradeToVer107,
 		upgradeToVer108,
+		upgradeToVer109,
 	}
 )
 
@@ -2191,6 +2194,15 @@ func upgradeToVer108(s Session, ver int64) {
 	doReentrantDDL(s, CreateTTLTableStatus)
 }
 
+// For users that upgrade TiDB from a 6.2-6.4 version, we want to disable tidb gc_aware_memory_track by default.
+func upgradeToVer109(s Session, ver int64) {
+	if ver >= version109 {
+		return
+	}
+	mustExecute(s, "REPLACE HIGH_PRIORITY INTO %n.%n VALUES (%?, %?);",
+		mysql.SystemDB, mysql.GlobalVariablesTable, variable.TiDBEnableGCAwareMemoryTrack, 0)
+}
+
 func writeOOMAction(s Session) {
 	comment := "oom-action is `log` by default in v3.0.x, `cancel` by default in v4.0.11+"
 	mustExecute(s, `INSERT HIGH_PRIORITY INTO %n.%n VALUES (%?, %?, %?) ON DUPLICATE KEY UPDATE VARIABLE_VALUE= %?`,
diff --git a/session/bootstrap_test.go b/session/bootstrap_test.go
index f7ced237b0170..087d5efdbcd09 100644
--- a/session/bootstrap_test.go
+++ b/session/bootstrap_test.go
@@ -1275,3 +1275,56 @@ func TestTiDBCostModelUpgradeFrom610To650(t *testing.T) {
 		}()
 	}
 }
+
+func TestTiDBGCAwareUpgradeFrom630To650(t *testing.T) {
+	ctx := context.Background()
+	store, _ := createStoreAndBootstrap(t)
+	defer func() { require.NoError(t, store.Close()) }()
+
+	// upgrade from 6.3 to 6.5+.
+	ver63 := version93
+	seV63 := createSessionAndSetID(t, store)
+	txn, err := store.Begin()
+	require.NoError(t, err)
+	m := meta.NewMeta(txn)
+	err = m.FinishBootstrap(int64(ver63))
+	require.NoError(t, err)
+	err = txn.Commit(context.Background())
+	require.NoError(t, err)
+	mustExec(t, seV63, fmt.Sprintf("update mysql.tidb set variable_value=%d where variable_name='tidb_server_version'", ver63))
+	mustExec(t, seV63, fmt.Sprintf("update mysql.GLOBAL_VARIABLES set variable_value='%s' where variable_name='%s'", "1", variable.TiDBEnableGCAwareMemoryTrack))
+	mustExec(t, seV63, "commit")
+	unsetStoreBootstrapped(store.UUID())
+	ver, err := getBootstrapVersion(seV63)
+	require.NoError(t, err)
+	require.Equal(t, int64(ver63), ver)
+
+	// We are now in 6.3, tidb_enable_gc_aware_memory_track is ON.
+	res := mustExec(t, seV63, fmt.Sprintf("select * from mysql.GLOBAL_VARIABLES where variable_name='%s'", variable.TiDBEnableGCAwareMemoryTrack))
+	chk := res.NewChunk(nil)
+	err = res.Next(ctx, chk)
+	require.NoError(t, err)
+	require.Equal(t, 1, chk.NumRows())
+	row := chk.GetRow(0)
+	require.Equal(t, 2, row.Len())
+	require.Equal(t, "1", row.GetString(1))
+
+	// Upgrade to 6.5.
+	domCurVer, err := BootstrapSession(store)
+	require.NoError(t, err)
+	defer domCurVer.Close()
+	seCurVer := createSessionAndSetID(t, store)
+	ver, err = getBootstrapVersion(seCurVer)
+	require.NoError(t, err)
+	require.Equal(t, currentBootstrapVersion, ver)
+
+	// We are now in 6.5.
+	res = mustExec(t, seCurVer, fmt.Sprintf("select * from mysql.GLOBAL_VARIABLES where variable_name='%s'", variable.TiDBEnableGCAwareMemoryTrack))
+	chk = res.NewChunk(nil)
+	err = res.Next(ctx, chk)
+	require.NoError(t, err)
+	require.Equal(t, 1, chk.NumRows())
+	row = chk.GetRow(0)
+	require.Equal(t, 2, row.Len())
+	require.Equal(t, "0", row.GetString(1))
+}