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The ZEUS (Zero Emission Ultimate Ship), developed in the framework of the national research project TecBia conducted by Fincantieri and co-founded by Italian Ministry of Economic Development, is a 25m length vessel characterized by a zero-emissions propulsion system. The on-board power generation is provided by 4 PEM Fuel Cell modules (140 kW power installation) fed by hydrogen stored into 48 Metal Hydride tanks (MH). PEMFC and MH thermal systems are coupled to recover the heat produced by PEMFC and to feed the endothermic dissociation reactions of hydrogen from MHs. This paper provides a Matlab-Simulink model to simulate the dynamic behaviour of the PEMFC power generation system and the thermal coupling with MH racks installed onboard. Three typical operative profiles are simulated to verify the thermal management control system and the impact of transient conditions on the propulsion plant. Furthermore, the effects of the major exogenous parameters are investigated. Results verify that thermal coupling between the two systems is guaranteed; however, an excessive load increase can lead the stacks to operate under non-optimal conditions for significant periods of time. The effect of exogenous parameters has been verified to be negligible and does not significantly affect the control system.