Molecular simulations were performed to characterize hydrated Nafion membranes in terms of gas adsorption, diffusion, and permeation. The experimental results validate the molecular model of Nafion with respect to material density, morphology, free volume, and water diffusivity. Nafion's adsorption property is examined in terms of the solubility and adsorption isotherms for gases, including H(2), O(2), and N(2). The adsorption capacity of hydrated Nafion is shown to be strong for O(2) and N(2) but not for H(2). Due to the dilution effect, N(2) is able to suppress the loading of O(2) and protect the fuel cell from fuel crossover. The dynamic behaviors of H(2) and O(2) are represented by self-diffusion coefficients, with the results showing that H(2) diffusion in Nafion membranes is nearly 1 order of magnitude faster than O(2) diffusion. The effects of water content and the concentration of adsorbed gases were verified, and a close correlation of Nafion free volume to gas transport properties was revealed. On the basis of the solution-diffusion mechanism, the permeabilities of H(2) and O(2) in hydrated Nafion membranes are calculated and compared with corresponding experiments, and the permeability of H(2) is found to be approximately twice that of O(2).