Abstract A hybrid energy system (HES) including hydrogen fuel cell systems (FCS) and a lithium-ion (Li-ion) battery energy storage system (ESS) is established for hydrogen fuel cell ships to follow fast load transients. An energy management strategy (EMS) with hierarchical control is presented to achieve proper distribution of load power and enhance system stability. In the high-control loop, a power distribution mechanism based on a particle swarm optimization algorithm (PSO) with an equivalent consumption minimization strategy (ECMS) is proposed. In the low-level control loop, an adaptive fuzzy PID controller is developed, which can quickly restore the system to a stable state by adjusting the PID parameters in real time. Compared with the rule-based EMS, hydrogen consumption is reduced by 5.319%, and the stability of the power system is significantly improved. In addition, the ESS degradation model is developed to assess its state of health (SOH). The ESS capacity loss is reduced by 2% and the daily operating cost of the ship is reduced by 1.7% compared with the PSO-ECMS without considering the ESS degradation.