Methods and Apparatus of managing decoded picture buffer for a video decoding system using Intra Block Copy (IBC) mode. In one embodiment, one or more previously reconstructed pictures after in-loop filtering are stored in a DPB (decoded picture buffer). For decoding a current picture, a first and a second picture buffers are allocated in the DPB. Both unfiltered version and filtered version of reconstructed current picture are stored in the first and second picture buffers. After the current picture is decoded, the unfiltered version is removed from the DPB. In another embodiment, an unfiltered version and filtered version of reconstructed current picture are stored. One of them is stored in the DPB and the other is stored in a temporary buffer. After the current picture is decoded, the unfiltered version is removed from the DPB or the temporary buffer.