Random disulfonated poly(arylene ether sulfone)-silica nanocomposite (FSPAES-SiO2) membranes were physicochemically tuned via surface fluorination. Surface fluorination for 30 min converted about 20% of the C-H bonds on the membrane surface into C-F bonds showing hydrophobicity and electronegativity at the same time. The membranes with hydrophobic surface properties showed high dimensional stability and low methanol permeability when hydrated for direct methanol fuel cell applications. In particular, the surface enrichment of fluorine atoms led to anisotropic swelling behavior, associated with a stable electrode interface formation. Interestingly, in spite of the use of a random copolymer as a polymer matrix, the low surface free energy of the C-F bonds induced a well-defined continuous ionic channel structure, similar to those of multiblock copolymers. In addition to the morphological transition, fluorine atoms with high electron-withdrawing capability promoted the dissociation of sulfonic acid (-SO3H) groups. Consequently, FSPAES-SiO2 membranes exhibited improved proton conductivity. Thus, FSPAES-SiO2 membranes exhibited significantly improved single-cell performances (about 200%) at a constant voltage of 0.4 V in comparison with those of Nafion 117 and nonfluorinated membranes. Surprisingly, their good electrochemical performances were maintained with very low nonrecovery loss over the time period of 1400 h and interfacial resistances 380% times lower than those of conventional membrane-electrode assemblies comprising the control hydrocarbon membrane and a Nafion binder for the electrodes.