Autophagy is an evolutionary conserved cellular process that delivers the intracellular components to lysosome for degradation and recycling, which is tightly regulated by multiple pathways. This catabolic process involves the renewal of organelles, the removal of misfolded proteins and protein aggregates as well as the elimination of pathogens in cells. Therefore, autophagy is critical to maintain cellular homeostasis and closely related to the development of many human diseases. With the deepening of the mechanism research of autophagy regulation, more and more deubiquitinating enzymes have been proved to play an important role in autophagy-related ubiquitin signaling system. These enzymes can act at different stages of autophagy, and target different ubiquitinated machinery components or substrates of autophagy. As the therapeutic targets for autophagy-related diseases including neurodegeneration diseases and tumors, deubiquitinating enzymes have attracted extensive attention. The discovery of various small-molecule inhibitors provides the possibility to further study the autophagy regulatory activity of the ubiquitinases and also the treatment of related diseases.