With the advancement of global energy conservation and emission reduction, hydrogen-powered ships (HPSs) have received great attention. However, the current drainage volume of HPSs is generally small, and its operating load fluctuates greatly due to the influence of hydrological and meteorological conditions in the waterway. Therefore, a reasonable energy management strategy (EMS) is needed to allocate the output of hydrogen fuel cells (HFCs) and lithium batteries (LBs). This article proposes a two-stage EMS framework for HPSs based on dynamic empirical modeling and model predictive control (DEM-MPC) to achieve optimal operational energy efficiency of the HFC-LB energy supply system. Firstly, a DEM probabilistic load forecasting (PLF) model was established by combining the operational status data of an HPS system with the meteorological data of waterway water level. The DEM model was constructed using delay coordinate embedding (DCE) and nearest neighbor prediction (NNP) methods to obtain future multi-step PLF sequences as important reference information for the EMS. Subsequently, the PLF sequence is used as input for MPC to optimize the output allocation of the EMS. In the first stage of MPC, the efficiency of HFCs and LBs is optimized, and in the second stage, the comprehensive cost is optimized. Finally, the method was validated using actual data from an HPS in the Yangtze River waterway. The results indicate that the proposed DEM-MPC framework significantly improves the overall operational energy efficiency of HPSs.