Organic sultones and a perfluorinated sultone are grafted on the surface of montmorillonite (MMT) to render the organic sulfonic acid (HSO3–) functionality. Organic–inorganic composite proton-conducting membranes are cast together with Nafion® using these functionalized MMTs as inorganic fillers. Grafting with the perfluorinated sultone is more efficient on the surface of MMT than with non-fluorine organic sultones. Montmorillonite functionalized with the perfluorinated organic sulfonic acid also shows higher ion exchange capacity and ion conductivity, which are desired attributes to serve as an effective filler for a proton-conducting composite membrane. The composite membrane reduces the relative permeability of methanol in 3M solution by about 40%, while maintaining comparable ionic conductivity relative to pristine Nafion membrane. This leads to much enhanced performance of a direct methanol fuel cell employing the Nafion®/sulfonated MMT composite membrane. The current density of a membrane-electrode assembly (MEA) fabricated with a composite membrane containing MMT functionalized with perfluorinated organic sulfonic acid is about 24% higher than that of a MEA fabricated with a composite membrane containing MMT functionalized with non-fluorine organic sulfonic acids, and about 40% higher than that with pristine Nafion®.