Objective To investigate the effect of inhibition the mitochondrial inner membrane protein OMA1 on rotenone-induced apoptosis in Parkinson's disease (PD) cell model. Methods SH-SY5Y cells were cultured in vitro, treated with Rot (final concentrations of 0.05, 0.1, 0.2, 0.3, 0.4 μmol/L) for 24 h, and the best Rot (0.2 μmol/L) was selected for subsequent experiments. The experiment was divided into control group (cells without special treatment), PD model group (0.2 μmol/L Rot treated cells for 24 h), Negative control group (negative control sequence of OMA1 siRNA transfected on the basis of normal control group), OMA1 siRNA group (0.2 μmol/L Rot treated cells for 24 h and transfected with OMA1 siRNA). CCK-8 was used to detect cell survival rate, inverted phase contrast microscope was used to observe cell morphology in each group, Western blot was used to detect changes in the expression of OMA1 and apoptosis-related proteins Caspase-3, Bax, and Bcl-2, and TUNEL apoptosis kit was used to detect cell apoptosis. Results Compared with the control group, the survival rate of SH-SY5Y cells decreased in a concentration-dependent manner with increasing Rot concentration (P<0.05). Compared with the control group, the expression of OMA1 and apoptotic protein Caspase-3 expression were increased and Bax/Bcl-2 values were increased in the PD model group (P<0.01). Compared with the PD model group, the cells in the OMA1 siRNA group, the OMA1 siRNA group gradually restored morphological changes, decreased apoptotic protein Caspase-3 expression and Bax/Bcl-2 values, and TUNEL apoptosis staining suggested reduced apoptosis (P<0.01). Conclusions Inhibition of the mitochondrial inner membrane protein OMA1 ameliorates apoptosis induced by the Rot-induced PD cell model, which in turn may have a protective effect on neurons.