The development of rapid and dependable proton transport channels is crucial for proton exchange membrane fuel cells (PEMFCs) operating in low humidity conditions. Herein, a metal–organic framework (NH-Zr framework) consisting of 1H-pyrazole-3, 5-dicarboxylic acid (PZDC), and zirconium chloride octahydrate (ZrOCl2·8H2O) rich in basic sites was in situ constructed in a perfluorosulfonic acid (PFSA) solution, and hybrid proton exchange membranes were prepared (PFSA-NH-Zr). The introduced NH-Zr framework successfully induced proton conducting groups (-SO3H) reorganization along the NH-Zr framework, resulting in the formation of fast ion transport channels. Meanwhile, under low humidity, the acid–base pairs between N–H (NH-Zr framework) and -SO3H (PFSA) promoted the protonation/deprotonation and the subsequent proton leap via the Grotthuss mechanism. Especially, the hybrid membrane PFSA-NH-Zr-1 with suitable NH-Zr content had a promising proton conductivity of 0.031 S/cm at 80 °C, 40% relative humidity (RH), and 0.292 S/cm at 80 °C, 100% RH, which were approximately 33% and 40% higher than the pristine PFSA membrane (0.023 S/cm and 0.209 S/cm), respectively. In addition, the maximum power density of the hybrid proton exchange membrane was 0.726 W/cm2, which was nearly 20% higher than the pristine PFSA membrane (0.604 W/cm2) under 80 °C, 40% RH. Thus, PFSA-NH-Zr may be promising membrane materials for potential applications in fuel cells. This work established a referable strategy for developing high-performance proton exchange membranes under low RH conditions.