The intrinsic relationship between proton conductivity, thermal stability and structural symmetries of phosphotungstic acid (HPW)-functionalized mesoporous silica (HPW-meso-silica) membrane was investigated with mesoporous silica from 2D hexagonal p6mm, 3D face-centered cubic (View the MathML source), body-centered View the MathML source, to cubic bicontinuous View the MathML source symmetries. HPW-meso-silica nanocomposites with 3D mesostructures display a significantly higher proton conductivity and higher stability as a function of relative humidity in comparison to 2D mesostructures. The best result was obtained with body-centered cubic (View the MathML source)-HPW-meso-silica, showing proton conductivities of 0.061 S cm−1 at 25 °C and 0.14 S cm−1 at 150 °C, respectively, and an activation energy of 10.0 kJ mol−1. At 150 °C, the cell employing a HPW-meso-silica membrane produced a maximum power output of 237 mW cm−2 in a methanol fuel without external humidification. The high proton conductivity and excellent performance of the new methanol fuel cells demonstrate the promise of HPW-meso-silica nanocomposites with 3D mesostructures as a new class of inorganic proton exchange membranes for use in direct methanol fuel cells (DMFCs).