In recent years, pure electric ship research has become a hot spot in the field of ship research, and lithium battery packs are a major difficulty in the research of pure power ships. Especially the life and safety problems of lithium battery packs seriously affect the future practical application of ships. Therefore, the energy storage system is designed as two sets of lithium battery packs. While increasing the energy of the energy storage system, the power supply of the battery pack is ensured, which not only ensures the safety of the pure electric ship, but also reduces the aging reaction rate of the lithium battery pack. Through the multi-energy ship modeling, specifically related to the control and safe operation of lithium battery packs, a lithium battery pack energy management strategy is provided. The specific scheme is: the model of ship sailing mileage and SOC is established by the theory of energy conservation, the lithium battery aging model is obtained by the lithium battery data of the actual pure electric ship navigation, and the lithium battery pack energy switching based on the mileage aging battery model is proposed. The strategy uses a logic threshold optimization algorithm to reduce the aging rate of the lithium battery pack. Finally, the experimental results show that the lithium battery pack with energy management strategy can perform 400 more navigations when the capacity loss reaches 15% in the same environment. It shows that this strategy is beneficial to improve the cycle life of lithium battery packs.