A molecular dynamics model was performed to study the proton transport of Nafion series membrane which is often used in low temperature fuel cells. The simulations intents to investigate the microstructure and the phenomenon of the proton transport processing. The model includes all-atom of main and side chains. The force field includes intermolecular Coulomb and Lennard-Jones terms and intra-molecular terms for harmonic bond stretch potentials, harmonic angle bend potentials and cosine terms for the torsions. The simulations were carried out in two cube systems at different temperature where water content differed from 5 and 10 water molecules per acid group in the polymer, respectively. The results showed that proton transport affected with water content by analyses of snap- shots of the MD simulation, the radial distribution functions between the sulfur atoms of SO3− groups, between the oxygen atoms of H3O+ ions, between oxygen atoms of water molecules and Nafion atoms at various stages.