This study describes the property of proton transfer in Nafion membrane analyzed by molecular dynamics (MD) simulation including both Vehicle and Grotthus mechanism. To treat Grotthus mechanism, Empirical Valence Bond (EVB) method was introduced to MD simulation. The potential energy barrier of proton hopping obtained by EVB method was adjusted to the computational result of Density Functional Theory (DFT). After adjusting EVB potential, it is confirmed that protons hop along the hydrogen bond network consecutively. The parameter for the simulation of Nafion membrane was water contents λ, which is defined as the ratio of water molecules and hydronium ions to sulfo groups, SO3-, obtained by λ=NH2O,H3O+/N SO3-. The changes of transferring properties and structure of molecules with the changes of λ were analyzed by Mean Square Displacement and Radial Distribution Function, respectively.