Abstract: The application of large-scale distributed energy storage systems (DESSs) can improve the redundancy and operational safety of ship microgrids. However, uncertain operating environments can easily lead to inconsistent characteristics of distributed energy storage. In this context, the paper proposes a two-layer energy management strategy for DESS of ships with state coupling constraints. First, considering the impact of uncertain shipping environments, an integrated model for shipboard energy storage states is established to quantify the state-of-power (SoP) range under different levels of state of health (SoH). Subsequently, the paper establishes a two-layer energy management strategy for DESS, combining long time-scale fuel economy scheduling with short time-scale power allocation strategy to mitigate the impact of uncertain navigation conditions. Finally, the proposed method is simulated in a hardware-in-the-loop (HiL) platform. Compared with two conventional methods, the proposed approach improves fuel economy by 20.8% and reduces voltage sag by 73.5%.