Assimilating hydrophilic hollow polymer spheres (HPS) into Nafion matrix by a loading of 0.5 wt % led to a restructured hydrophilic channel, composed of the pendant sulfonic acid groups (–SO₃H) and the imbedded hydrophilic hollow spheres. The tiny hydrophilic hollow chamber was critical to retaining moisture and facilitating proton transfer in the composite membranes. To obtain such a tiny cavity structure, the synthesis included selective generation of a hydrophilic polymer shell on silica microsphere template and the subsequent removal of the template by etching. The hydrophilic HPS (100–200 nm) possessed two different spherical shells, the styrenic network with pendant sulfonic acid groups and with methacrylic acid groups, respectively. By behaving as microreservoirs of water, the hydrophilic HPS promoted the Grotthus mechanism and, hence, enhanced proton transport efficiency through the inter-sphere path. In addition, the HPS with the –SO₃H borne shell played a more effective role than those with the –CO₂H borne shell in augmenting proton transport, in particular under low humidity or at medium temperatures. Single H₂-PEMFC test at 70°C using dry H₂/O₂ further verified the impactful role of hydrophilic HPS in sustaining higher proton flux as compared to pristine Nafion membrane.