Abstract: Polar code is a new research hotspot in the field of channel coding due to its high reliability and lower encoding and decoding complexity, and it can reach the Shannon capacity limit in theory. The ongoing researches on Polar codes have provided numerous code construction algorithms and decoding methods for several kinds of channel types and application fields. However, the theoretic proofs and the performances of Polar codes in underwater acoustic (UWA) channels are relatively less concerned. In this paper, a Polar code channel coding mechanism is established, which matches the UWA channel with significant multipath, strong Doppler spreading, limited bandwidth, and other complex random transmission characteristics. Then the performance of Polar codes is studied in the UWA communication system with the orthogonal frequency division multiplexing (OFDM) technique by theoretical analysis and simulation. Meanwhile, the BER performances of Polar codes under different UWA channel models, channel parameters, code lengths, and code rates are also compared. The simulation results show that the BER of Polar codes with a code rate of 1/2 in the underwater time-varying channel can reach 10^-4~10^-5 when the signal-to-noise ratio (SNR) is 4 dB, which is about 0.5~1 dB better than LDPC and Turbo codes. The results demonstrate that the proposed mechanism matches the UWA channel well, thus the application of Polar codes is suitable and reliable in UWA communication systems.