Metal–organic framework (MOF) nanofillers have attracted significant attention recently for high-temperature proton exchange membrane fuel cell (HT-PEMFC) applications because of their excellent effectiveness for enhancing the performance of proton exchange membranes (PEMs) based on phosphoric acid–doped polybenzimidazole (PBI). Universitetet i Oslo-66 (UiO-66) is one of the most used zirconium-based MOFs. In this study, we synthesized amine-functionalized UiO-66, imidazole-functionalized UiO-66, and sulfonated UiO-66 as nanofillers for adjusting the interfacial compatibility of PBI-based nanocomposite membranes. The results demonstrated that incorporating functionalized UiO-66 nanocrystals simultaneously improved tensile strength, oxidative stability, and proton conductivity of the membranes. Moreover, the imidazole-functionalized UiO-66 nanofiller exhibited optimal interfacial compatibility with polybenzimidazole and more significantly improved membrane properties than the other nanofillers. The PEM containing 10 wt% imidazole-functionalized UiO-66 achieved a 113% increase in proton conductivity at 170°C (0.0418 S/cm) and a 249% increase in the maximum power density of the fuel cell (406.1 mW/cm2).