A hydrogen fuel cell ship needs to carry a great amount of hydrogen as the fuel, which powers the ship but simultaneously poses threats on ship's safety because of the hydrogen's leakage- and explosion-proneness properties. This study focused on a hydrogen fuel cell ship, and we established the corresponding geometrical model. In case of the occurrence of hydrogen explosion, hydrogen leakage was first calculated based on the leakage model; then, using the ANSYS fluent (a fluid computation software), the hydrogen's diffusion process in various compartments was simulated and the variation of hydrogen concentration distribution with the leakage time was concluded. Finally, numerical simulations were conducted under different conditions when the ignition source appeared in the fuel cell compartment, the control compartment and the passenger compartment, respectively, and the overpressure and high-temperature damages induced by the explosion were analyzed in detail. The present simulations on leakage and explosion of hydrogen can help us to obtain more details on the consequences after the accident, and thereby we could propose the appropriate design scheme, management method and escape measures to reduce the risk of leakage accidents on the ship and enhance the safety of HFCSs.