In this paper, the thermal conductivity of dry Nafion 117 is measured by Hot Disk TPS2500 and a molecular dynamics calculation model for the proton exchange membrane is constructed by Materials Studio (MS) software platform to study its thermal conductivity. Cell structures of different water content of Nafion membrane at 300 K and 330 K are obtained, respectively. It is found that at the same temperature the predicted thermal conductivity of PEM increases with the water content, and at the same water content the predicted thermal conductivity decreases with the temperature. So both the water content and temperature are important factors affecting thermal conductivities of PEM.