These days Polymer Electrolyte Fuel Cell (PEFC) is the most developed fuel cell. A polymer electrolyte membrane (PEM) is used in PEFC. Its efficiency is proportional to the proton transferring efficiency, which depends on the nanoscale structure of water. In this study, the property of proton transfer was analyzed by Molecular Dynamics (MD) method including Grotthus mechanism by Empirical Valence Bond (EVB) method. Nafion membrane was adopted as PEM. The potential energy barrier of proton hopping obtained by EVB method was adjusted to reproduce the energy barrier obtained by Density Functional Theory (DFT). In MD simulation, the distribution of water in Nafion was firstly analyzed. The results showed that liquid molecules gather around sulfo groups. Next, the property of proton transfer was analyzed by Mean Square Displacement (MSD).