Encoding methods and apparatuses include receiving input video data of a current block in a current picture and applying a Cross-Component Adaptive Loop Filter (CCALF) processing on the current block based on cross-component filter coefficients to refine chroma components of the current block according to luma sample values. The method further includes signaling two Adaptive Loop Filter (ALF) signal flags and two CCALF signal flags in an Adaptation Parameter Set (APS) with an APS parameter type equal to ALF or parsing two ALF signal flags and two CCALF signal flags from an APS with an APS parameter type equal to ALF, signaling or parsing one or more Picture Header (PH) CCALF syntax elements or Slice Header (SH) CCALF syntax elements, wherein both ALF and CCALF signaling are present either in a PH or SH, and encoding or decoding the current block in the current picture.