The complexity of the underwater environment poses a challenge to underwater acoustic communication, the high rate and reliable transmission of underwater communication is achieved by optimizing channel estimation technology. In this paper, the filter bank multicarrier/offset quadrature amplitude modulation (FBMC/OQAM) modulation technology is introduced underwater, the channel estimation technology in the FBMC/OQAM system is studied, and the discrete pilot channel estimation algorithm is studied in detail. This paper analyzes the performance of discrete pilot channel estimation under the influence of different channels, and improves the problem of excessive power consumption of the auxiliary pilot method. An improved auxiliary pilot method (IAP) is proposed to reduce the power consumption, it also improves the estimated performance. Theoretical analysis and simulation results show that the IAP algorithm proposed in this paper is a good choice for the practical application of underwater acoustic communication.