A series of new Nafion-based composite membranes have been prepared via an in situ sol-gel reaction of 3-(trihydroxylsilyl)propane-1-sulfonic acid and solution casting method. The morphological structure, ion-exchange capacity, water uptake, proton conductivity, and methanol permeability of the resulting composite membranes have been extensively investigated as functions of the content of sulfopropylated polysilsesquioxane filler, temperature, and relative humidity. Unlike the conventional Nafion/silica composites, the prepared membranes exhibit an increased water uptake and associated enhancement in proton conductivity compared to unmodified Nafion. In particular, considerably high proton conductivities at 80 and 120 degrees C under 30% relative humidity have been demonstrated in the composite membranes, which are over 2 times greater than that of Nafion. In addition to a remarkable improvement in proton conductivity, the composite membranes display lower methanol permeability and superior electrochemical selectivities in comparison to the pure Nafion membrane. These unique properties could be exclusively credited to the presence of pendant sulfonic acid groups in the filler, which provides fairly continuous proton-conducting pathways between filler and matrix in the composite membranes and thus facilitates the proton transport without the anticipated trade-off between conductivity and selectivity. This work opens new opportunities of tailoring the properties of Nafion-the benchmark fuel cell membrane-to obviate its limitations and enhance the conductive properties at high temperature/low humidity and in direct methanol fuel cells.