The synthesis and characteristics of high-temperature proton-exchange membranes based on mesoporous silica nanocomposite functionalized with phosphotungstic acid (HPW) were investigated in detail for applications in proton-exchange membrane fuel cells (PEMFCs) and direct methanol fuel cells (DMFCs). The HPW–meso-silica nanocomposites were characterized by small-angle X-ray scattering (SAXS), FTIR spectroscopy, Raman spectroscopy, TGA, N2 absorption isotherm, water uptake, TEM, conductivity, and fuel cell performance. The spectroscopy results indicate interactions between the Keggin anions of HPW and meso-silica and the possible formation of (≡SiOH2
+)(H2PW12O40
–) species. The results show that the proton conductivity of the HPW–meso-silica nanocomposites depends strongly on the content of HPW. The threshold for the proton conductivity of the nanocomposite is ∼10 wt %. The best proton conductivity is 0.07 S cm–1 at 25 °C under 100% relative humidity (RH) with an activation energy of ∼14 kJ mol–1, obtained on HPW–meso-silica nanocomposites with 67–83% HPW. A PEMFC based on a HPW–meso-silica membrane produced a power output of 308 mW cm–2 at 80 °C and 80% RH in H2/O2, 206 mW cm–2 at 80 °C and 80% RH in H2/air, and 134 mW cm–2 at 160 °C in methanol/air without external humidification. The high tolerance of HPW–meso-silica nanocomposites toward RH fluctuations demonstrates the unique high water retention capability of HPW–meso-silica nanocomposites. The results indicate that HPW–meso-silica forms a promising proton-exchange membrane for PEMFCs and DMFCs operating at high temperatures.