Aiming to solve the problems of insufficient dynamic responses, the large loss of energy storage life of a single power cell, and the large fluctuation in DC (direct current) bus voltage in fuel cell vessels, this study takes a certain type of fuel cell ferry as the research object and proposes an improved equivalent minimum hydrogen consumption energy management strategy, based on fuzzy logic control. First, a hybrid power system including a fuel cell, a lithium–iron–phosphate battery, and a supercapacitor is proposed, with the simulation of the power system of the modified mother ship. Second, a power system simulation model and a double-closed-loop PI (proportion integration) control model are established in MATLAB/Simulink to design the equivalent hydrogen consumption model and fuzzy logic control strategy. The simulation results show that, under the premise of meeting the load requirements, the control strategy designed in this paper improves the Li-ion battery’s power, the Li-ion battery’s SOC (state of charge), the bus voltage stability, and the equivalent hydrogen consumption significantly, compared with those before optimization, which improves the stability and economy of the power system and has certain practical engineering value