diff --git a/config/config.go b/config/config.go
index 1ba2c7fbd1595..ac7b63584c019 100644
--- a/config/config.go
+++ b/config/config.go
@@ -49,7 +49,8 @@ const (
 	// DefTxnEntrySizeLimit is the default value of TxnEntrySizeLimit.
 	DefTxnEntrySizeLimit = 6 * 1024 * 1024
 	// DefTxnTotalSizeLimit is the default value of TxnTxnTotalSizeLimit.
-	DefTxnTotalSizeLimit = 100 * 1024 * 1024
+	DefTxnTotalSizeLimit        = 100 * 1024 * 1024
+	SuperLargeTxnSize    uint64 = 100 * 1024 * 1024 * 1024 * 1024 // 100T, we expect a txn can never be this large
 	// DefMaxIndexLength is the maximum index length(in bytes). This value is consistent with MySQL.
 	DefMaxIndexLength = 3072
 	// DefMaxOfMaxIndexLength is the maximum index length(in bytes) for TiDB v3.0.7 and previous version.
diff --git a/session/session.go b/session/session.go
index 3dd2f6a09bd68..93139522830f4 100644
--- a/session/session.go
+++ b/session/session.go
@@ -3684,6 +3684,11 @@ func (s *session) GetStmtStats() *stmtstats.StatementStats {
 // SetMemoryFootprintChangeHook sets the hook that is called when the memdb changes its size.
 // Call this after s.txn becomes valid, since TxnInfo is initialized when the txn becomes valid.
 func (s *session) SetMemoryFootprintChangeHook() {
+	if config.GetGlobalConfig().Performance.TxnTotalSizeLimit != config.DefTxnTotalSizeLimit {
+		// if the user manually specifies the config, don't involve the new memory tracker mechanism, let the old config
+		// work as before.
+		return
+	}
 	hook := func(mem uint64) {
 		if s.sessionVars.MemDBFootprint == nil {
 			tracker := memory.NewTracker(memory.LabelForMemDB, -1)
diff --git a/tidb-server/main.go b/tidb-server/main.go
index 9b1e58b736844..5895cac6b099f 100644
--- a/tidb-server/main.go
+++ b/tidb-server/main.go
@@ -628,7 +628,12 @@ func setGlobalVars() {
 	}
 	plannercore.AllowCartesianProduct.Store(cfg.Performance.CrossJoin)
 	privileges.SkipWithGrant = cfg.Security.SkipGrantTable
-	kv.TxnTotalSizeLimit = cfg.Performance.TxnTotalSizeLimit
+	if cfg.Performance.TxnTotalSizeLimit == config.DefTxnTotalSizeLimit {
+		// practically deprecate the config, let the new session memory tracker take charge of it.
+		kv.TxnTotalSizeLimit = config.SuperLargeTxnSize
+	} else {
+		kv.TxnTotalSizeLimit = cfg.Performance.TxnTotalSizeLimit
+	}
 	if cfg.Performance.TxnEntrySizeLimit > 120*1024*1024 {
 		log.Fatal("cannot set txn entry size limit larger than 120M")
 	}