This research aimed to study the application of magnetic resonance imaging (MRI) under three-dimensional mark point positioning algorithm in stereotactic surgery for Parkinson’s disease (PD) and improve clinical treatment effect. Eighty patients with PD in Tianjin Medical University General Hospital were selected as the research objects and randomly divided into two groups. The three-dimensional mark point positioning algorithm was applied to perform feature positioning on the MRI images of PD patients, and the international unified Parkinson’s disease rating scale (UPDRS) was assessed before and after single-target surgery of the two groups. There was a significant difference in the postoperative treatment effect between the two groups compared with the preoperative one ( P < 0.05 ). Among the patients in the observation group, 37 cases were marked as markedly effective, accounting for 92.5% of the total group; 1 case was ineffective and 2 cases were improved, accounting for 2.5% and 5%, respectively. In the control group, 35, 2, and 3 cases were assessed as markedly effective, ineffective, and improved, accounting for 87.5%, 5%, and 7.5%, respectively. The overall curative effect of the observation group was better than that of the control group, and the difference was significant ( P < 0.05 ). The MRI manifestations of PD patients were diversified. MRI under the three-dimensional mark point positioning algorithm had a high value for the stereotactic treatment of PD patients, which was beneficial to the clinical surgery.