To simulate the PVC agglomerate phenomenon in proton exchange membrane fuel cell (PEMFC) cathode, we established 3D two-phase micro-structure lattice models, including C phase (Pt/C particles) and IP phase (mixed ionomer and pore), respectively. Based on these models, we studied the effect of Pt/C agglomerates on theoretical catalyst utilization, IP phase tortuosity and cell performance in PEMFC, and compared the electrode with linear agglomerates to the electrode with spherical agglomerates. Unexpectedly, contrary to the simulation results from macro-models, the electrode with Pt/C linear agglomerates performed better than that with Pt/C spherical agglomerates. In addition, it was found that the electrode with Pt/C agglomerates performed better than that without Pt/C agglomerates, which was different to what we believed before. By analysing the reasons of cell performance change, it was found that mass transport had a more important effect on cell performance than electrochemical reaction. (C) 2017 Hydrogen Energy Publications LLC. Published by Elsevier Ltd. All rights reserved.