The revolutionary functionally gradient proton exchange membranes were fabricated by EB irradiation with heterogeneous energy deposition. These heterogeneous energy deposition profiles (Depth-Dose profiles) were simulated by Monte Carlo simulation code EGS5. In the process of EB-grafting method of styrene onto base fluorinated polymer, the energy depositions selected from the Depth-Dose profiles were used. The grafted membranes were sulfonated with chlorosulfonic acid in carbon tetrachloride. The DOGs in the direction of thickness showed that EB Depth-Dose profiles corresponded to the EB grafting reaction. The functionally gradient proton exchange membranes had a water uptake gradient in the direction of depth, and hence could be a promising solution to manage water behavior in Membrane Electrode Assembly (MEA) of Polymer Electrolyte Fuel Cell (PEFC).