The increasing demand for decarbonization of marine transportation motivates the utilization of low-carbon resources. Among different options, fuel cells are drawing attention. The selection of fuel cell (FC) and the design of energy management strategy would have a great impact on the vessel's operational efficiency, and thereby needs to be considered carefully. The objective of this paper is to develop energy management system (EMS) to reduce the fuel consumption of a hybrid fuel cell/battery ship. To this end, a day-ahead EMS scheme is proposed that takes full use of information including ship cruising routines and the degradation status of the fuel cell modules. The developed EMS is optimization-based and conducted off-line to provide guideline for the next-day power generation plan. In addition, three power allocating strategies across the multiple fuel cell modules are considered and compared (equal, independent, and sequential). A sequential rotation procedure is proposed to reduce the degradation rates of the fuel cell modules. Simulation results show that the proposed EMS can effectively improve the fuel economy of the hybrid ship while enhancing sufficient energy backup throughout the full voyage. In addition, comparisons between different FC configurations implies that the independent distribution has the highest fuel efficiency, and with the proposed rotation procedure, the sequential distribution can effectively improve the fuel efficiency by up to 23.2%.