To spread polymer electrolyte fuel cells, improving the cell performance is required. The cell performance depends on various factors. One of the factors that lowers cell performance is proton transport resistance in catalyst layers. Catalyst layers have multiscale structures which influence on proton transport resistance. In this study, to investigate the relationship between structures of catalyst layers and cell performances, mass transport and chemical reactions are calculated in the 3D catalyst layer models. The information about the ionomer thickness dependence on the diffusion coefficient of protons based on the molecular dynamics simulation is introduced to transport calculation in order to analyze nanoscale structure influence on the cell performance. As a result, we have found that the output voltage increases over the whole range of current density with increasing ionomer/carbon ratio considering ionomer thickness dependence. This result suggests that the nanoscale structure in catalyst layer has a large influence on the cell performance. Furthermore, cell performance analysis with ionomer thickness distribution based on experimental values is conduced in this study. The result suggests that contribution of nanoscale proton transport characteristic increases by improving the ionomer distribution model.