Abstract Background Parkinson’s disease (PD) is a neurodegenerative disease characterized by progressive loss of dopaminergic neurons. UBC9 is related to the formation of several cancers. Nevertheless, the function of UBC9 in PD and the potential mechanisms are vague. Methods MPP⁺-induced SH-SY5Y cells and MPTP-treated C57BL/6 mice were applied to induce PD models. Cell viability, proliferation and apoptosis were measured using CCK-8, EdU and Annexin V/PI staining, respectively. JC-1 staining and fluorescent probes DCFH-DA were employed to measure mitochondrial membrane potential and ROS production. The SOD, GSH and MDA content were determined by the commercially kits. SUMOylation of PINK1 were predicted by SUMOplot and verified by co-IP/Western blot. Mitophagy-related proteins, SUMO enzymes, and TH were analyzed by qRT-PCR/Western blot. LC3 expression was detected via immunofluorescence staining. Transmission electron microscopy was performed to detect autophagy. MPTP-induced brain injury was evaluated using Nissl staining, IHC and TUNEL assay. Motor function was observed via open field test and pole test. Results PINK1 and UBC9 were low-expressed in MPP + -induced SH-SY5Y cells. UBC9 mediated PINK1 SUMOylation. UBC9 overexpression promoted cell viability and reduced cells apoptosis in MPP + -stimulated SH-SY5Y cells, which was reversed after PINK1 silence or CsA treatment. Moreover, UBC9 overexpression counteracted MPP + -induced mitophagy, and oxidative stress. However, these findings were reversed by CsA or PINK1 silencing. PINK1 bound SUMO1 at the K522, K363 and K193 sites, further regulating cells viability and apoptosis. In MPTP-treated mice, UBC9 overexpression alleviated mitochondrial dysfunction and motor deficits via PINK1 SUMOylation. Conclusion UBC9 mediated mitophagy to attenuate MPP + /MPTP-induced neurotoxicity and oxidative stress by regulating PINK1 SUMOylation, suggesting that UBC9 may play a preventive role in PD progression.