A three-dimensional, non-isothermal and two-phase flow model for proton exchange membrane (PEM) fuel cells is developed. In the cathode catalyst layer, a spherical agglomerate model with consideration of catalyst layer structure and liquid water effect is applied to determine the electrochemical kinetics. The size and structure of the agglomerates are determined by the following parameters, i.e., the agglomerate radius (r(agg)), the volume fraction of ionomer within the agglomerate (L-i,L-agg), and the thickness of the ionomer film over the agglomerate (delta(i)) It is noted that a random combination of the three above parameters is widely used in agglomerate models by researchers. In this paper, the effects of r(agg), and L-i,L-agg on the cell performance and local transport characteristics are numerically investigated by using the developed model with consideration of the relationships between agglomerate parameters. It is concluded that the cell performance is significantly improved by decreasing r(agg) and increasing L-i.agg at medium and high current densities when the volume fractions of the solid phase (L-pt/c) and ionomer phase (L-i) are maintained constant. In addition, the distributions of oxygen concentration, liquid water saturation, volumetric current density and effectiveness factor are also strongly influenced by the variation of the two parameters. (C) 2018 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.