The transfer processes of reactants and products affect each other in proton exchange membrane fuel cells (PEMFCs), because they have contrast transfer directions between flow channels and gas diffusion layers (GDLs). In this study, a two-dimensional, two-phase, non-isothermal and steady state model is developed to analyze the species transportation behaviors through diffusion and convection in PEMFCs with orientated-type flow channels. Five conventional shape baffles effects on mass transfers are compared, and the relationships between convection and diffusion of reactants and produced water vapor are discussed. Simulation results reveal that baffle shapes affect the mass transportation through the baffles leading angles and volumes, and larger leading angles enhance the reactants and the water vapor convective transferring into GDLs; meanwhile, larger baffle volumes enhance the reactant transferring into GDLs and water vapor transferring out from GDLs through diffusion processes. In addition, transportation processes of reactants and vapor affect each other, where more reactants convectively transferring into GDLs causes more water vapor entering GDLs; enhancing the reactants diffusively transferring into GDLs reduces water vapor diffusive transportation out from GDLs.