Polymer Electrolyte Fuel Cells (PEFCs) are expected to be used for automobiles and various applications because of their high power density and low environmental load. To spread PEFCs, improving cell performance is required. One of the factors that lowers cell performance is proton transport resistance in catalyst layers (CLs) which depends on CLs structure. Typical CLs are constructed by carbon supported Pt nanoparticles covered with ionomer thin films. Ionomer thin films have two important roles. First, ionomer thin films work as a binder between carbon black particles. Second, ionomer thin films provide path way for protons, so that proton transport resistance decreases with increasing ionomer carbon ratio (I/C). Oxygen transport resistance is another reason to lower cell performance. In CLs, oxygen transport involves the transport in micro porous media and the permeation through ionomer thin film, thus oxygen transport resistance increases with increasing I/C. To improve cell performance, both protons and oxygen transport resistance need to be low by the optimization of CLs structure. In this study, to analyze the relationship between cathode CLs structure and proton transport property, three-dimensional catalyst layer model is constructed considering carbon black aggregate and ionomer thickness distribution. Mass transport is calculated based on multi-block model considering proton diffusion, oxygen diffusion, water diffusion, and electrical conduction (1). And cathode reaction is calculated by Butler-Volmer equation. Inoue et al. analyzed the relationship between cell performance and CLs structure using the same model. They reported that oxygen transport resistance tends to be dominant for cell performance. However, they didn’t consider ionomer thickness dependence on proton transport property. In our previous study, we analyzed thickness dependence on proton transport properties of ionomer thin films using molecular dynamics (MD) simulations (2). Ionomer thin film was modeled as Nafion and water molecules adsorbed on flat carbon surface. The thickness of films was changed systematically from four nm to ten nm by changing the number of Nafion chains. Diffusion coefficient of protons was calculated with different ionomer thicknesses. It was found that at low water content, proton diffusion coefficients show a peak at the ionomer thickness of around seven nm. In this study, to analyze proton transport phenomena in detail, information about the relationship between ionomer thickness and diffusion coefficient of protons obtained from MD simulations has been introduced to the multi-block model as a correction term. It was found that gradient of I-V curve decreases with increasing I/C considering the correction term. This results suggest that the contribution of proton transport resistance increases considering nanoscale phenomena. In the future work, we will analyze mass transport properties in CLs such as the details of the overvoltage and current density distribution to investigate the relationship between CLs structure and proton transport properties. Acknowledgment This research was supported by the New Energy and Industrial Technology Development Organization (NEDO) of Japan and the Promotion of Science (JSPS) KAKENHI Grant no. 18H01364. We used the integrated supercomputation system at the Institute of Fluid Science.