Method and apparatus of video encoding video coding for a video encoder or decoder using Neural Network (NN) are disclosed. According to one method, input data or a video bitstream are received for blocks in one or more pictures, which comprise one or more colour components. The residual data, prediction data, reconstructed data, filtered-reconstructed data or a combination thereof is derived for one or more blocks of said one or more pictures. A target signal corresponding to one or more of the about signal types is processed using a NN (Neural Network) and the input of the NN or an output of the NN comprises two or more colour components. According to another method, A target signal corresponding to one or more of the about signal types is processed using a NN and the input of the NN or an output of the NN comprises two or more colour components.