A three-dimensional, non-isothermal mathematical model is developed for proton exchange membrane (PEM) fuel cells with conventional and interdigitated flow fields. The detailed heat/mass transfer and the electrochemical reactions of reactants in fuel cells are considered in this model, and the emphasis is placed on the electro-osmotic drag and the diffusion effects of liquid water in membrane, and the species transport and distribution in porous media. The effects of transport limit of oxygen and water content in membrane on local current density distributions of electrodes are analyzed and discussed. The results indicate that the interdigitated design of flow channel enhances the mass transport of gases in porous media and improves the output performance of fuel cell. However, the reduction of water at the interface of cathode catalyst layer can also deteriorate the hydration degree of membrane, which requires more effective water management to keep membrane from dehydrated.