As newly emerging proton-conducting materials, metal-organic frameworks (MOFs) have been attracting wide attention in the field of proton exchange membrane fuel cells. However, for most of the MOF materials, long-term stability is a huge obstacle for practical applications. So, the structural stability of MOFs is the critical prerequisite for the design and development of modified materials with excellent proton conductivity. In this review, stable UiO-66 derivatives were chosen as the research object, and modification methods including post-synthesis modification and hybridization were mainly summarized. Based on the reported typical functionalization strategies, we found that the modified UiO-66 derivatives and their composite membranes demonstrate ultra-high proton conductivity similar to that of commercial Nafion, indicating their great application potential in fuel cells. This Frontier article focuses on the recent development in the modification of UiO-66 type frameworks and their composite membranes and the tuning of proton conductivity with structural factors.