Abstract Ubiquitin-like 3 (UBL3) is a membrane-anchored protein that has been discovered to function as a protein post-translational modifier, helping to sort proteins into small extracellular vesicles (sEVs). Aggregations of alpha-synuclein (α-syn) are associated with the pathology of neurodegenerative diseases such as Parkinson’s disease (PD). The aggregation and toxicity of α-syn can be influenced by its interactions with specific proteins. Recently, the interactions between UBL3 and α-syn was uncovered. It is believed to play a role in eliminating excess α-syn from neurons, or in the spread of α-syn pathology in the brain associated with neurodegenerative diseases. However, the regulator that can mediate the interaction between UBL3 and α-syn remains unclear. In this study, we employed the split gaussian luciferase complementation assay and RNA interference (RNAi) technology to discover that QSOX2, HTATIP2, UBE3C, MGST3, NSF, HECTD1, SAE1 and ATG3 are involved in downregulating the interaction between UBL3 and α-syn. Among these proteins, silencing MGST3 had the most significant impact on the UBL3-α-syn interaction (with a fold change log2 of less than - 1). MGST3 is a part of the antioxidant system, and silencing MGST3 is believed to contribute to oxidative stress. We used hydrogen peroxide (H 2 O 2 ) to induce oxidative stress and observed its effect on the UBL3-α-syn interaction. Our finding showed that an 800μM concentration of H 2 O 2 could also downregulate this interaction. However, the effect of oxidative stress caused by 800μM H 2 O 2 on the UBL3-α-syn interaction did not be enhanced by silencing MGST3. In conclusion, the interaction between UBL3 and α-syn is downregulated by silencing MGST3.