Video processing methods and apparatuses include receiving input data associated with a current picture composed of multiple Coding Tree Units (CTUs) for encoding or decoding, partitioning the current picture into multiple subpictures, determining one or more reference pictures for inter coding the current picture, and encoding or decoding one or more blocks in one or more CTUs of the current picture by inter coding using the one or more reference pictures. Each of the reference pictures used for inter coding the current picture has a same CTU size as that of the current picture when the reference picture is not an Inter Layer Reference Picture (ILRP) containing one subpicture.