Hydrogen energy, with zero-carbon emissions and high energy density, shows promise for maritime decarbonization. This study focuses on energy efficiency analysis and design for hydrogen-powered vessels, exploring hydrogen fuel cell (HFC) operation principles and ship propulsion system coupling. An integrated mathematical model of HFCs and propulsion systems was developed to simulate interactions. By refining parameters and improving algorithms, we proposed a simplified EEDI calculation method tailored for hydrogen ships, building on the conventional EEDI framework. Using MATLAB, dynamic HFC models, thermodynamic cooling/lubrication models, and a ship resistance model were constructed. Input data combined theoretical calculations with real-ship measurements, ensuring applicability to newbuilds and existing vessels. The study innovatively enabled rapid EEDI computation and optimization for hydrogen ships by simulating resistance and energy consumption under varying conditions, validating the model’s accuracy and practicality. This research provides a theoretical foundation and simulation platform for hydrogen ship energy efficiency assessment, guiding low-carbon maritime technology development.