A two-dimensional, multiphase, non-isothermal numerical model was used to investigate the effect of the high performance catalyst layer (CL) design. Microstructure-related parameters were studied on the basis of the agglomerate model assumption. A conventional CL design (uniform Pt/C composition, e.g., 40wt%) was modified into two sub-layers with two different Pt/C compositions (in this study, 40 and 80wt%). The performance of sub-layers with different CL designs is shown to be different. Simulation results show that substituting part of the Pt/C 40wt% with Pt/C 80wt% increases the cell performance. It was found that factors including proton conductivity, open circuit voltage, and sub-layer thickness have a significant impact on overall cell performance. Different water distribution for different membrane electrode assembly designs was also observed in the simulation results. More liquid water accumulation inside the membrane electrode assembly is seen when the Pt/C 80wt% sub-layer is next to the gas diffusion layer. Finally, several key design parameters for the proposed high performance CL design including agglomerate radius, Nafion thin film thickness, and the Nafion volume fraction within the agglomerate in terms of CL fabrication were identified on the basis of our simulation results. Copyright (c) 2014 John Wiley & Sons, Ltd.