Nanomaterials with a uniform size, large surface area, high adsorption capacity, and excellent dispersion are critical to proton conduction and cell performance when functionalized and incorporated into a proton exchange membrane. We designed and fabricated a novel composite PEM based on vinylphosphonic acid-functionalized mesoporous silica nanoparticles (VPA-MSNs), with the aim of improving the cell performance and proton conductivity of a perfluorosulfonic acid (PFSA) membrane under low relative humidity (RH) conditions. The experimental results show that the VPA-MSN(–NH₂)/PFSA composite membrane provides a proton conductivity of up to 23.2 mS cm⁻¹ at 30% RH and up to 9.6 mS cm⁻¹ at 10% RH, which are respectively 3.2 and 8.6 times higher than those of a pristine PFSA membrane, and 5.6 and 10.4 times higher than those of a commercial Nafion membrane. In addition, the VPA-MSN(–NH₂)/PFSA composite membrane exhibits superior fuel cell performance and low ohmic resistance at low relative humidity. Improvements in water absorption/retention, proton conductivity, and single-cell performance resulted from these effectively hydrophilic surfaces and mass transfer pathways, as the mesoporous structure and abundant functional groups in the membrane enhanced the connectivity of the hydrophilic zone, forming new proton transport channels. The incorporation of VPA-MSNs into the PFSA matrix also enhanced the water retention properties and mechanical strength, and adjusted the organic–inorganic interface and hydrophilic ionic domains inside the membranes simultaneously. The results indicate that this new type of VPA-MSN(–NH₂)/PFSA composite membrane is promising for developing PEMs that tolerate variations in humidity.