Encoding methods and apparatuses include applying a Cross-Component Adaptive Loop Filter (CCALF) processing on a current picture based on CCALF coefficients signaled in one or more Adaptive Loop Filter (ALF) Adaptation Parameter Sets (APSs) to refine one or more chroma components according to a luma component, signaling two ALF signal flags and two CCALF signal flags in each ALF APS or parsing two ALF signal flags and two CCALF signal flags from each ALF APS, and encoding or decoding the current picture. Values of the two ALF signal flags and the two CCALF signal flags in each ALF APS are not all equal to 0 to ensure none of the ALF APS is an empty APS.