According to the significant effect of the structure and saturation of cathode catalyst layer (CCL) on the operation of proton exchange membrane fuel cell (PEMFC), a pore scale model is presented to simulate the transport processes in CCL. Using this model, the tortuosity and macroscopic effective diffusivity of CCL with different porosities and saturation levels were obtained. The water distribution was obtained by solving two-phase flow equations using volume of fluid (VOF) method. The structure of CCL was reconstructed by assuming agglomerates as equally-sized circles and spheres in two-and three-dimensional domains, respectively. A sequential algorithm was used to determine the location of agglomerates in the computational domain with specific overlap. A comparison was made between the results obtained for three- and two-dimensional domains which showed 2D assumption results in an overestimating on effective diffusivity. However, the variation trend of effective diffusivity versus porosity was about the same. According to the results, due to the blocking effect of water presence in CCL, the increase of saturation causes less available pathways for gas to diffuse. Therefore, the effective diffusivity decreases by the increase of saturation level. Moreover, the decrease of porosity leads to the increase of tortuosity which results in lower pathways for gas to diffuse into the domain and hence less effective diffusivity was obtained. The decrease of oxygen effective diffusivity of CCL causes a lack of oxygen concentration at the electrochemical reaction sites and leads to the decrease of the PEMFC performance.