This paper describes characteristics of proton transfer in polymer electrolyte membrane by Molecular Dynamics (MD) simulation. Nafion was used as a membrane. Grotthus mechanism as well as Vehicle mechanism was considered in the simulation. To treat Grotthus mechanism, Empirical Valence Bond (EVB) method was used. The parameters or functions of the interaction potential of EVB method were determined so that potential energy barrier of proton hopping obtained by EVB method is consistent with that obtained by Density Functional Theory (DFT) and adjusted so that the diffusion coefficient of hydronium ion in water obtained by MD simulation is consistent with that of experimental results. After annealing the system, radial distribution function or mean square displacements of hydronium ion and water, which correspond to diffusivity of each compound, was obtained. These results show the nanoscale characteristics of proton transfer in polymer electrolyte membrane.