The interfacial structure between ionomer (Nafion) and catalyst strongly influences oxygen reduction reaction 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 with various thicknesses. We revealed that hydrophilic domain in Nafion thin-films decreased with decrease of the thickness, reducing the proton conductivity.