A method and apparatus for video coding incorporating enhanced multiple transform (EMT) are disclosed. According to one method, the number of candidates for EMT in the horizontal direction or vertical direction is reduced depending on the current block size. According to another method, an EMT flag, one or more EMT indices or both are signalled only if the total number of non-zero coefficients in at least a part of the 2D coefficient block is greater than a threshold, where the threshold is equal to 1 or larger. A method and apparatus for video coding using non-separable secondary transform (NSST) are disclosed. According to this method, a total number of non-zero first coefficients in a partial block of the 2D coefficient block is determined and used to determine whether to apply the NSST process.