A model in which the reaction parameters of catalyst layers from microscopic to macroscopic scales are the main focus was systematically developed for polymer electrolyte fuel cells (PEFCs). The effect of oxygen-containing species adsorbed on the Pt surface at the microscopic three-phase boundary (Q(ox)), which suppresses the oxygen reduction reaction (ORR), was taken into account in the PEFC model. Q(ox) was expressed as a reaction parameter in terms of the coverage factor, and was included in the Tafel reaction equation. The advantages of our model were verified by carrying out the model validation, in which the results of cell performance obtained by simulation agreed very well with experimented results. Because of this key improvement, the developed model was more realistic and accurate. The simulation results also demonstrates that the effect of adsorbed oxygen-containing species is a very important reaction parameter that influences cell performance and must be considered in order to achieve high-performance PEFCs.