diff --git a/executor/set.go b/executor/set.go
index 2396356c1245b..a7b5ff19da91c 100644
--- a/executor/set.go
+++ b/executor/set.go
@@ -284,7 +284,16 @@ func (e *SetExecutor) getVarValue(ctx context.Context, v *expression.VarAssignme
 	if err != nil || nativeVal.IsNull() {
 		return "", err
 	}
-	return nativeVal.ToString()
+
+	value, err = nativeVal.ToString()
+	if err != nil {
+		return "", err
+	}
+
+	// We need to clone the string because the value is constructed by `hack.String` in Datum which reuses the under layer `[]byte`
+	// instead of allocating some new spaces. The `[]byte` in Datum will be reused in `chunk.Chunk` by different statements in session.
+	// If we do not clone the value, the system variable will have a risk to be modified by other statements.
+	return strings.Clone(value), nil
 }
 
 func (e *SetExecutor) loadSnapshotInfoSchemaIfNeeded(name string, snapshotTS uint64) error {
diff --git a/server/tidb_test.go b/server/tidb_test.go
index e8ffadc4fcdfa..11c31354ca0e9 100644
--- a/server/tidb_test.go
+++ b/server/tidb_test.go
@@ -2950,3 +2950,40 @@ func TestSandBoxMode(t *testing.T) {
 		require.NoError(t, err)
 	}
 }
+
+// See: https://github.com/pingcap/tidb/issues/40979
+// Reusing memory of `chunk.Chunk` may cause some systems variable's memory value to be modified unexpectedly.
+func TestChunkReuseCorruptSysVarString(t *testing.T) {
+	ts := createTidbTestSuite(t)
+
+	db, err := sql.Open("mysql", ts.getDSN())
+	require.NoError(t, err)
+	defer func() {
+		require.NoError(t, db.Close())
+	}()
+
+	conn, err := db.Conn(context.Background())
+	require.NoError(t, err)
+	defer func() {
+		require.NoError(t, conn.Close())
+	}()
+
+	rs, err := conn.QueryContext(context.Background(), "show tables in test")
+	ts.Rows(t, rs)
+
+	_, err = conn.ExecContext(context.Background(), "set @@time_zone=(select 'Asia/Shanghai')")
+	require.NoError(t, err)
+
+	rs, err = conn.QueryContext(context.Background(), "select TIDB_TABLE_ID from information_schema.tables where TABLE_SCHEMA='aaaa'")
+	ts.Rows(t, rs)
+
+	rs, err = conn.QueryContext(context.Background(), "select @@time_zone")
+	require.NoError(t, err)
+	defer func() {
+		require.NoError(t, rs.Close())
+	}()
+
+	rows := ts.Rows(t, rs)
+	require.Equal(t, 1, len(rows))
+	require.Equal(t, "Asia/Shanghai", rows[0])
+}