In a method and apparatus for video coding using Low-Frequency Non-Separable Transform (LFNST) mode, a coding unit (CU) is partitioned into one or more transform blocks (TBs). A syntax is determined at an encoder side or at a decoder side, where the determining step is performed by signaling the syntax at the encoder side or by parsing the syntax at the decoder side if one or more conditions are satisfied. The syntax indicates whether the LFNST mode is applied to the current CU and/or which LFNST kernel is applied when the LFNSF is applied, and the conditions comprise a target condition corresponding to that all target TBs in a target TB set have a TS mode indication as false, and the target TB set is selected from the TBs in the current CU. The current CU is encoded or decoded according to the LFNST mode.