A method for video encoding and decoding using Low-Frequency Non-Separable Transform (LFNST) mode and apparatus thereof are disclosed. The input data correspond to primary transformed data at the encoder and the input data correspond to coded data of the current CU at the decoder. A CU is partitioned into one or more transform blocks (TBs). An LFNST syntax is determined at an encoder side or at a decoder side if one or more conditions are satisfied. The LFNST syntax indicates whether the LFNST mode is applied to the current CU and/or which LFNST kernel is applied when the LFNST mode is applied. The conditions comprise the CBF indications for the target TBs being false. The current CU is encoded or decoded according to the LFNST mode as indicated by the LFNST syntax.