The shallow water acoustic (SWA) channel is one of the most challenging channels in wireless digital communications. In this paper, we propose a good performance, low complexity channel coding scheme using quasi-cyclic LDPC (QC-LDPC) codes to improve the communication system reliability for SWA channels. A system simulation model including QC-LDPC codes for the SWA channels is built. With the decoding algorithm of belief propagation (BP), the effects of QC-LDPC codes design parameters, such as girth, circulant permutation matrix size and decoding iterations are discussed. To verify the proposed approach, Quangang Xiaocuo harbor blasting data are used to set up a SWA channel model, and the performances of QC-LDPC codes over the channel model are analyzed. The results show that, with the same parameters, the proposed QC-LDPC channel coding strategy for SWA channels substantially outperforms the conventional (3, 6)-LDPC channel coding strategy, and with less complexity and easy implementation.