In this work, a novel nanocomposite material, hollow mesoporous silica nanosphere impregnated with 12-phosphotungstic acid, briefed as HMSN-I, was synthesized by a vacuum-assisted impregnation method. The HMSN-I was used as an inorganic filler to synthesize Nafion-based composite membranes for the high temperature and low humidity operation of proton exchange membrane fuel cells (PEMFCs). The Nafion/HMSN-I composite membrane showed much higher conductivity than the pristine Nafion membrane under the identical conditions. The cell with the Nafion/HMSN-I composite membrane demonstrated significantly enhanced cell performance and stability in high temperature and low humidity environment. The mechanism can be ascribed to the enhanced proton conductivity and water retention ability of the composite membrane, which is very promising for the development of high temperature and low humidity PEMFCs.