We have proposed a model of Nafion membrane based on DREIDING force field validated by comparing the density, water diffusivity, and Nafion morphology with experimental data. The simulated final density agrees with experiment within 1.3 % for various water contents. In addition to determination of diffusion coefficients of liquid molecules as a function of hydration level for dynamical validation, we have also calculated static structure factors among liquid molecules for mesoscopic structural validation. The diffusion coefficient of water molecules is found to be in good agreement with experimental data. The diffusion coefficient of hydronium ions has showed that general trends in the experimental data are reproduced although the classical models have the limitation of hydronium dynamics. The static structure factors of liquid molecules at low wave length provide insights into the periodic structure of the inter-clusters which are consistent with the experimental data based on small-angle X-ray and neutron scattering.