Video processing methods and apparatuses implemented in a video encoding or decoding system with conditional secondary transform signaling. The video encoding system determines and applies a transform operation to residuals of a transform block to generate final transform coefficients, and adaptively signals a secondary transform index according to a position of a last significant coefficient in the transform block. A value of the secondary transform index is determined according to the transform operation. The video decoding system parses last significant coefficient position syntax of each transform block in the current block from a video bitstream to determine a position of a last significant coefficient for each transform block, and infers inverse secondary transform is not applied to the current block according to the positions of the last significant coefficients; otherwise, the video decoding system determines an inverse transform operation by parsing a secondary transform index from the video bitstream.