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S-PEEK has been known as one of the promising candidates for fuel cell application since it has high thermo-oxidative stability and extraordinary mechanical properties as well as high cost effectiveness. However, the nanoscale structure and transport properties for S-PEEK have not been thoroughly reported at molecular level. Through this study, we have investigated the the nanophase-segregated structure of hydrated S-PEEK membrane using atomistic molecular dynamics simulation method. We will present the effect of water content and temperature on the nanophase-segregation and water transport of the hydrated S-PEEK membrane. The simulation results for the S-PEEK membrane are discussed in comparison with the experimental data available in the literatures as well as those for the Nafion membrane.