Non-coding RNA plays an important role in the occurrence and development of Parkinson’s disease (PD). This study only explores the diagnostic value of miR-431-5p in PD and its role in the development of PD. A total of 92 patients with PD were selected as the PD group, and 100 healthy individuals undergoing physical examinations were selected as the control group. The levels of serum miR-431-5p were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR). The receiver operating characteristic (ROC) curve was drawn to evaluate the diagnostic value of serum miR-431-5p for PD. Multivariate Logistic regression was utilized to analyze the risk factors of PD with cognitive impairment. The in vitro PD cell model was constructed by inducing SH-SY5Y cells with MPP+, and the effects of miR-431-5p on the proliferation, apoptosis, inflammation, oxidative stress and autophagy of the cell model were explored. Luciferase reporter gene was used to evaluate the interaction between miR-431-5p and its downstream target genes. The expression of miR-431-5p in PD is decreased, and its expression in PD with cognitive impairment is lower than that in PD without cognitive impairment. The diagnostic value of miR-431-5p combined with α-Syn for PD is better than that of a single indicator. Logistics regression analysis demonstrated that total unified Parkinson’s disease rating scale (UPDRS) and miR-431-5p were the risk factors for the occurrence of PD with cognitive impairment. In vitro studies have shown that MPP+ induces the inhibition of proliferation and the promotion of apoptosis, autophagy, inflammation and oxidative stress. However, the above effects can be offset by the addition of miR-431-5p mimics. SOX9 is a direct target gene of miR-431-5p, which is upregulated in PD. miR-431-5p is down-regulated in PD and has clinical significance for the early diagnosis of PD. miR-431-5p may play a role in the progression of PD by targeting SOX9.