Oxygen diffusion and reduction in the catalyst layer of PEM fuel cell is an important process in fuel cell modelling, but models able to link the reduction rate to catalyst-layer structure are lack; this paper makes such an effort. We first link the average reduction rate over the agglomerate within a catalyst layer to a probability that an oxygen molecule, which is initially on the agglomerate surface, will enter and remain in the agglomerate at any time in the absence of any electrochemical reaction. We then propose a method to directly calculate distribution function of this probability and apply it to two catalyst layers with contrasting structures. A formula is proposed to describe these calculated distribution functions, from which the agglomerate model is derived. The model has two parameters and both can be independently calculated from catalyst layer structures. We verify the model by first showing that it is an improvement and able to reproduce what the spherical model describes, and then testing it against the average oxygen reductions directly calculated from pore-scale simulations of oxygen diffusion and reaction in the two catalyst layers. The proposed model is simple, but significant as it links the average oxygen reduction to catalyst layer structures, and its two parameters can be directly calculated rather than by calibration.