In this study, molecular dynamic simulation method was employed to study the structure and transport properties of Aquivion in comparison to Nafion. From experimental and computational work, there is a general consensus that the favored properties of Polymer electrolyte membrane (PEM) system are a result of nano-phase segregation of hydrophilic clusters in a hydrophobic matrix. Aquivion has a similar chemical structure to Nafion with hydrophobic backbone and hydrophilic sulfonate group. As such, we investigate the structure formed by Aquivion, to check for the desired nanophase segregation, when simulated in conditions similar to fuel cell conditions of temperature and humidity. We also characterize water diffusion and proton transport in this segregated structure, and compared them with hydrated Nafion membrane system.