The decoding throughput during post-processing is one of the major bottlenecks that occur in 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-MET-LDPC) codes using a graphics processing unit (GPU) in continuous-variable quantum key distribution (CV-QKD) systems. As described herein, we optimize the storage methods related to the parity check matrix, merge the sub-matrices which are unrelated, and decode multiple codewords in parallel on the 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 64.11 Mbits/s, 48.65 Mbits/s and 39.51 Mbits/s, respectively, when decoding 128 codewords of length [Formula: see text] simultaneously without early termination.