During the assembly of a fuel cell, the mechanical stress and strain that occur have a significantly large effect on the performance and reliability of fuel cell. When assembling a fuel cell stack, the assembly pressure generated can decrease the interfacial contact resistance (ICR) between the bipolar plate (BPP), gas diffusion layer (GDL) and catalyst layer, and also, the reduction in mass transfer that happens during the electrochemical reaction in the catalyst layer through the GDL must be considered. Recent research on the numerical analysis of fuel cells does not take into account the aforementioned importance of the GDL compression deformation, claiming the restrictions of numerical analysis, and uses a simple model to analyze the mass transfer of the fuel cells using CFD analysis. Therefore in this research, the performance of the fuel cell (e.g. pressure drop, gas permeability of GDL, and the electrolyte membrane water content (lambda) were compared for the FSI model, which is a thermal fluid based PEMFC model (CFD model) that takes the GDL compression deformation into account. The GDL compression deformation, dependent on the fuel cell assembly pressure, affects the gas permeability caused by under-rib convection. As a result in the inlet of the fuel cell, the internal pressure and flow velocity increase due to the decrease in cross sectional area, but due to the decreased gas permeability of the rib it has a low current density, and as the outlet is approached, it can be determined that the current density actually increases due to the hydrogen and oxygen mass fractions being greater than the CFD model making the current density more uniform overall. Therefore using the FSI analysis method, it is important to predict the optimized fuel cell architecture and operating condition parameters.