As differentiated from conventional synthetic processes, amino-functionalized hollow mesoporous silica (NH2–HMS) has been synthesized using a new and facile strategy of ion-exchange-induced selective etching of amino-functionalized mesoporous silica (NH2-meso-silica) by an alkaline solution. Nuclear magnetic resonance (NMR) spectroscopy and in situ time-resolved small-angle X-ray scattering (SAXS) reveal that ion-exchange-induced selective etching arises from the gradient distribution of OH– in the NH2-meso-silica nanospheres. Moreover, the ion-exchange-induced selective etching mechanism is verified through a successful synthesis of hollow mesoporous silica. After infiltration with phosphotungstic acid (PWA), PWA–NH2–HMS nanoparticles are dispersed in the poly(ether sulfone)–polyvinylpyrrolidone (PES–PVP) matrix, forming a hybrid PWA–NH2–HMS/PES–PVP nanocomposite membrane. The resultant nanocomposite membrane with an optimum loading of 10 wt % of PWA–NH2–HMS showed an enhanced proton conductivity of 0.175 S cm–1 and peak power density of 420 mW cm–2 at 180 °C under anhydrous conditions. Excellent durability of the hybrid composite membrane fuel cell has been demonstrated at 200 °C. The results of this study demonstrated the potential of the facile synthetic strategy in the fabrication of NH2–HMS with controlled mesoporous structure for application in nanocomposite membranes as a technology platform for elevated-temperature proton exchange membrane fuel cells.