We consider the application of protograph-based low density parity check (LDPC) codes with a remarkable reduction encoding time relative to MacKay's LDPC codes for underwater acoustic (UWA) channels. It's observed that the conventional protograph-based LDPC codes, e.g. AR4JA, which have excellent performance in AWGN channels may not accomplish in UWA channels as well when the code lengths of them are short. In this paper, we propose a protograph LDPC code to adopt the UWA channels which suffer from severe inter-symbol interference (ISI) produced by long multipath delay spreading and bandwidth extremely limited by acoustic propagation loss. The simulation results show that the proposed code outperforms MacKay's (3, 6) LDPC codes by O.SdB and the rate-1/2 of AR4JA code by over ldB with 2048 bits code length in the NSVG and ISVG underwater channels, at near to 10−5 of the BER. In addition, over the two UWA channel models, the performances of the proposed code in BER do not degrade obviously when code lengths are decreasing. Consequently, the proposed code is a good alternative code to improve the operation speed, reliability and robustness of UWA communication system.