Methods and apparatus for coding system incorporating AMT (adaptive multiple core transform) for the chroma transform blocks (TBs) are disclosed. According to one method, one or more flags are signaled to indicate whether AMT can be applied for the chroma TBs. If the one or more flags indicate that AMT can be applied for the chroma TBs, the chroma TBs can use the same or separate AMT selection information as the corresponding Luma TB. According to another method, when AMT and the transform skip mode are both available for use for a transform block, the on/off signaling of AMT is coded before the on/off signaling of the transform skip mode. The on/off signaling of the transform skip mode is not coded if the coded AMT on/off flag is true. The on/off signaling of the transform skip mode can be inferred to be false if not coded.