Polymer electrolyte fuel cells (PEFCs) are highly expected as a next-generation power supply system due to the purity of its exhaust gas, its high power density and high efficiency. The polymer electrolyte membrane is a critical component for the performance of the PEFCs and it is important to understand the nanostructure in the membrane to enhance proton transport. We have performed an atomistic analysis of the vehicular transport of hydronium ions and water molecules in the nanostructure of hydrated Nafion membrane by systematically changing the hydration level which provides insights into a connection between the nanoscopic and mesoscopic structure of ion clusters and the dynamics of hydronium ions and water molecules in the hydrated Nafion membrane. In this study, classical molecular dynamics simulations are implemented using a model of Nafion membrane which is based on DREIDING force field and newly modified and validated by comparing the density, water diffusivity, and Nafion morphology with experimental data. The simulated final density after the annealing procedure agrees with experiment within 1.3% for various water contents and the trends that density decreases with increasing hydration level are reproduced. In addition to determination of diffusion coefficients of solvent molecules as a function of hydration level (from λ = 1 up to λ = 18), we have also calculated radial distribution functions and static structure factors not only to clarify the structure of water molecules and hydronium ions around the first solvation shell of sulfonate groups but also to validate the mesoscopic periodic structure among water clusters. The diffusion coefficient of water molecules increases with increasing hydration level and 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 by the simulations although the classical models have the limitation of probing hydronium dynamics. The static structure factors of liquid molecules at low wave length provide insights into the periodic structure of the inter-water clusters. These results are consistent with the Gebel's model based on small-angle X-ray scattering that considers the dry membrane to be made of isolated spherical ionic clusters of radius ∼7.5 Å that swell with increasing hydration.