In order to reduce the total cost of fuel cell vehicles, catalysts for polymer electrolyte fuel cells (PEFCs) have been developed in recent years. However, these catalysts have been developed by trial-and-error methods and the correlation between catalyst nature and output performance is still not clear. Our goal is to reduce the catalyst cost by analyzing the key factors affecting the output performance in catalyst layers (CLs). In our previous studies, a method for reaction and mass transport simulation in the through-plane directionwas established. Additionally, electrochemical reactions and radial mass transport phenomena in the catalyst with primary particle size were simulated in this study. The results suggest that the characteristics of Pt particles such as diameter and bearing position mainly affect the output performance at high voltages (0.7-0.9 V). Furthermore, the rate-determining step for the catalyst with primary particle size was the oxygen diffusion step in the ionomer.