The decoding throughput in the postprocessing is one of the bottlenecks for a continuous-variable quantum key distribution (CV-QKD) system. In this paper, we propose a layered decoder to decode quasi-cyclic multi-edge type LDPC (QC-METLDPC) codes based on graphic processing unit (GPU) in continuous-variable quantum key distribution (CV-QKD) systems. We optimize the storage method of the parity check matrix, merge the sub-matrices which are unrelated, and decode multiple codewords in parallel on GPU. Simulation results demonstrate that the average decoding speed of LDPC codes with three typical code rates, i.e., 0.1, 0.05 and 0.02, is up to 64.11Mbits/s, 48.65Mbits/s and 39.51Mbits/s, respectively, when decoding 128 codewords of length 106 simultaneously without early termination.