Quasi cyclic LDPC (QC-LDPC) codes consisting of circulant permutation matrices (CPM-QC-LDPC) are one of the most attractive types of LDPC codes due to their many advantages. In this paper, we mainly do some research on CPM-QC-LDPC codes. We first propose a two-stage decoding scheme mainly based on parity check matrix transform (MT), which can efficiently improve the bit error rate performance. To optimize the tradeoff between hardware implementation complexity and decoding performance, an improved method that combines our proposed MT scheme with the existing CPM-RID decoding scheme is presented. An experiment shows that both schemes can improve the bit error rate (BER) performance. Finally, we show that the MT decoding mechanism can be applied to other types of LDPC codes. We apply the MT scheme to random LDPC codes and show that it can efficiently lower the error floor.