Methanol crossover of the direct methanol fuel cells (DMFCs) deteriorates the performance dramatically. It is essential to investigate the transport phenomena inside the electrolyte. This paper presents an atomistic model based on the molecular dynamics (MD) technique. The molecular system considered in this simulation includes the solid electrolyte (Nafion117®), methanol molecules, hydroniums and water contents. Those water molecules are attracted by the sulfonic acid group (SO3-) of the polymer electrolyte. Methanol molecules were found to migrate with water molecules and hydroniums due to the electrostatic force. Crossover phenomena of methanol molecules at different methanol concentrations were also investigated to observe the methanol effect on the proton migration. Simulation results indicate that the methanol molecules tend to distribute in the vicinity of the hydrophobic site compared with water. The relationship between the calculated diffusion coefficient of hydroniums and the methanol concentration shows that methanol assists the transport of hydroniums.