Heteropoly acids (HPAs) have been used in perfluorinated sulfonic acid polymers such as Nafion or Aquivion to form organic/inorganic composite membranes with improved proton conductivity and water management ability. However, the HPA has a low BET surface area with water-soluble characteristics, which prevents enhancement in the number of proton-transferable sites and accelerates HPA leaching while operating the proton exchange membrane fuel cells (PEMFCs). The HPA was functionalized on zeolite imidazolate framework-67 (ZIF-67) nanoparticles to address these drawbacks. Incorporating it into the MOF made it water insoluble and enhanced the internal surface area, leading to a good proton conductor. Using a synthetic approach, we were able to form HPA-functionalized ZIF-67 (HZF), which can be optimized with simple compositional modifications and whose HPA content is controllable. The HZF nanoparticles exhibited a hollow structure that formed an HPA−ZIF shell layer because the dissociated cobalt ion and 2-methylimidazole diffused from the core side to the surface layer to interact with the HPA. The HZF/Aquivion composite membranes exhibited excellent mechanical properties and good resistance to the polymer chain swelling phenomenon. The electrochemical properties of the HZF/ Aquivion composite membranes with various HZFs were characterized to determine the optimal HPA content in the HZF nanoparticles. The 3 wt % hollow HZF/Aquivion composite membrane with the appropriate HPA content exhibited higher proton conductivities than the pure Aquivion membrane, measuring 0.14 S/cm at 25 °C and 100% RH and 0.09 S/cm at 80 °C and 30% RH. This result indicates that the hollow HZF/Aquivion composite membrane can provide efficient proton transfer and water management ability, suggesting a good strategy for the PEMFC operation.