The interfacial structure between ionomer (Nafion®) and catalyst strongly influences oxygen reduction reaction kinetics in polymer electrolyte fuel cells. Therefore, understanding the correlation between the interfacial structure and electrochemical properties is important to design the reaction field with high activity. In this research, we examined the morphology and proton conductivity of the Nafion thin-films on Pt electrode with various thicknesses and annealing treatment. We revealed that the proton conductivity of Nafion thin-film is influenced by the hydrophilic ordered structure in the Nafion thin-films by using grazing incidence small-angle scattering (GISAXS) technique