The design and preparation of proton-conducting metal-organic frameworks (MOFs) with superconductivity are of significance for the proton-exchange membrane fuel cell (PEMFC). Introducing functional structural defects to enhance proton conductivity is a good approach. Here, we synthesized a series of UiO-66 (first synthesized in the University of Oslo) with missing-linker defects and investigated the effect of defect numbers on the proton conductivity of the samples. Among them, 60-UiO-66-1.8 (60 represents the synthesis temperature and 1.8 the number of defects) prepared with 3-mercaptopropionic acid as a modulator has the best proton conductivity, which is 3 × 10-2 S cm-1 at 100 °C and under 98% relative humidity (RH). The acidic sites induced by missing-linker defects further promote the chemisorption of ammonia molecules, resulting in the formation of a richer hydrogen-bond network and hence boosting the proton conductivity to 1.04 × 10-1 S cm-1 at 80 °C, which is one of the highest values among the reported MOF-based proton conductor. Therefore, this work provides a new strategy for enhancing proton conduction in MOF-based materials.