ABSTRACT A one-dimensional, steady-state, two-phase, isothermal numerical simulations were performed to investigate the effect on cell performance of a PEM fuel cell under non-uniform porosity of gas diffusion layer. In the simulation, the non-uniform porosity of gas diffusion layer was taken into account to analyze the transport phenomena of water flooding and mass transport in the gas diffusion layer. The porosity of the gas diffusion layer is treated as a linear function. Furthermore, the structure of the catalyst layer is considered to be a cylindrical thin-film agglomerate. Regarding the distribution analysis of liquid water saturation, oxygen concentration and water concentration depend on the porosity of gas diffusion layer. In the simulation, the ε CG and ε GC represent the porosity of the interfaces between the channel and gas diffusion layer and the gas diffusion layer and the catalyst layer, respectively. The simulation results indicate that when the (ε CG , ε GC ) = (0.8, 0.4), higher liquid water saturation appears in the gas diffusion layer and the catalyst layer. On the contrary, when the (ε CG , ε GC ) = (0.4, 0.4), lower liquid water saturation appears. Once the liquid water produced by the electrochemical reaction and condensate of vapor water may accumulate in the open pores of the gas diffusion layer and reduced the oxygen transport to the catalyst sites. This research attempts to use a thin-film agglomerate model, which analyze the significant transport phenomena of water flooding and mass transport under linear porosity gradient of gas diffusion layer in the cathode of a PEM fuel cell