The International Maritime Organization (IMO) has been continuously strengthening environmental regulations to reduce greenhouse gas emissions from ships, which has led to increased attention on hybrid ship propulsion systems combining hydrogen fuel cells and batteries. This study analyzes the energy management strategy of a hybrid ship propulsion system in relation to changes in the battery system’s energy capacity. The target vessel was set as a 500 kW-class ferry operating for 24 h, and the maximum current rate (C-rate) and effects of the equivalence factor, which are key elements of the energy management problem, in relation to changes in energy capacity were investigated. The results show that while changes in the battery system’s energy capacity do not significantly affect the optimal operating point of the hybrid ship propulsion system, they are highly influenced by the response speed of the hydrogen fuel gas supply system and fuel cells, as well as the maximum C-rate required by the battery system. Furthermore, the equivalence factor, one of the key parameters in the optimization problem, tends to vary depending on the degree of charging and discharging, as it affects the equivalent fuel consumption of the battery system.