In order to clarify the proton transport phenomena in Nafion/carbon nanotubes (CNTs) composite membranes, we focused on the interfacial transport between Nafion and graphene sheets (GSs). We investigated the water content dependence of proton transport and structural properties at the interface between Nafion and GSs using molecular dynamics simulations. The density distribution, water cluster analysis at the interface region, and the self-diffusion coefficient of protons at the interface region were obtained at different water contents. The self-diffusion coefficients of protons at the interface were larger than those of the Nafion bulk for all the water contents because of the formation of water layer near the interface. Our findings provide insight into the relationship between the proton transport and the interfacial structure at molecular level, which suggests a possible improvement on proton transport with addition of CNTs with high specific surface area.