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The effects of ship vibrations on the mass transfer and performance of proton exchange membrane fuel cells (PEMFCs) have many vague aspects. Hence, the method of loading ship vibrations with the sliding mesh is first proposed in this paper. Furthermore, this method is adopted to form the solution of the simulation study of PEMFC performance under ship vibrations. In the framework of computational fluid dynamics, the ship vibration is loaded into the three-dimensional PEMFC model and successfully solved. Then, a series of special cases are performed to explore the gas distribution and output features of PEMFCs in ship environments with different vibrations. Finally, the results show that the ship vibrations have vectorial effects on the gas transfer in the PEMFC. Additionally, vibrations perpendicular to the channel evidently affect the gas transfer. Moreover, while the vibrations are parallel to the channel, they remain nearly normal. Relatively, a more significant influence on the output voltage of the PEMFC will occur under smaller frequencies and/or greater amplitudes of ship vibrations., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)