Pipeline conflicts arising from data dependencies are a common issue encountered in the hardware implementation of layered QC-LDPC decoders. This paper proposes an efficient layered decoding architecture to reduce pipeline conflicts without introducing stall cycles, by reordering the processing order offline and using the patch method based on variable-to-check message. The experimental results on the LDPC code of the IEEE802.16 standard in the OFDM-PON system demonstrate that the proposed architecture has a sensitivity improvement of 0.125 dBm and 0.375 dBm, respectively, compared with our previous work and the method described in the other work.