Proton conductivity of polyelectrolytes in the interfacial region with a solid is key to the performance of polyelectrolyte-based fuel cells. The proton conductivity of Nafion thin films was examined as a function of the thickness along both directions, normal and parallel to the interface. Neutron reflectivity measurements revealed that a water-containing multilamellar structure was formed at the substrate interface. The presence of the interfacial layer, or the two-dimensional proton-conductive pathway, suppressed and enhanced the out-of-plane and in-plane proton conductivities, respectively. The method of proton conductivity in the interfacial region differed from that in the bulk, namely, the Grotthuss mechanism. Using laminated films, we conclude by showing that the proton conductivity in the Nafion thin film changes on the basis of the interface-to-volume ratio. This knowledge will be helpful for the design of devices containing polyelectrolytes with solid materials.