Protons transfer in polyelectrolyte membrane by both Vehicle and Grotthus mechanisms. This study describes the property of proton and water transfer in perfluorosulfonic acid (PFSA) membrane using molecular dynamics (MD) simulation in view of both Vehicle and Grotthus mechanisms. To treat Grotthus mechanism, Empirical Valence Bond (EVB) method was introduced to MD simulation. The potential energy barrier of proton hopping in EVB method was adjusted to the computational result of Density Functional Theory (DFT) to replicate the experimental value of diffusion coefficient of oxonium ions in water. The transport property of water and oxonium ions in PFSA membrane was analyzed by such as Radial Distribution Function (RDF) and Mean Square Displacement (MSD) at different water contents. From this analysis, some perception of the structure of water cluster and the diffusivity of water and proton in PFSA membrane was derived.