Nafion and poly(vinylidene fluoride trifluoroethylene) (PVDF-TrFE) blend membranes are introduced for realizing the controlled nanostructure of the membrane for high proton conduction. In particular, PVDF-TrFE which shows dipole polarization between fluorine and hydrogen atoms can be aligned by thermal annealing conditions. In this research, the crystalline morphology of the blend membranes of Nafion/PVDF-TrFE are carefully controlled by melt-recrystallization of PVDF-TrFE molecules, allowing the chain rotation from the edge-on to the face-on structure. The through-plane proton conduction from anode to cathode is demonstrated with a highly aligned nanostructure of Nafion/PVDF-TrFE molecules for high-performance fuel cell operation.