The interactions of hydronium and water with nafion(R) membrane are relevant in proton transfer process in nafion(R), a fuel cell electrolyte membrane. To investigate such crucial actions, molecular dynamic simulations were studied in this work using a model consisting of nafion(R) side chains cluster with water molecules and hydronium ions comparing with dry system. After simulations, the trajectories were analyzed in term of intermolecular distances, potential energy, and radial distribution function. In addition, quantum calculations were investigated to clarify the role of hydronium ions and water in proton transfer manner.