Objective To explore the application value of time of flight magnetic resonance angiography (TOF-MRA) in target bypass surgery for moyamoya disease. Methods The data of patients with moyamoya disease in Affiliated Drum Tower Hospital, Medical College, Nanjing University between May 1 and August 30, 2020 were retrospectively analyzed. Patients were divided into navigation group and control group according to whether navigation technology was used during operation. All patients completed TOF-MRA evaluation before operation, and all patients completed surgical treatment. One week after operation, TOF-MRA was reviewed to evaluate the patency of anastomotic stoma. The intraoperative and postoperative conditions of the two groups were compared. Results Finally, 48 patients with moyamoya disease were included. 22 patients who used intraoperative navigation were included in the navigation group, and 26 patients with moyamoya disease who did not use intraoperative navigation in the same period were included in the control group. There was no significant difference between the two groups in gender, age, Suzuki stage before operation, proportion of posterior circulation involvement, proportion of bleeding type, proportion of hypertension and proportion of diabetes (P>0.05). The operation duration [(3.3±0.4) vs. (3.6±0.6) h] and postoperative hospital stay [(7.3±1.9) vs. (8.8±2.7) d] in the navigation group were shorter than those in the control group (P<0.05). There was no significant difference between the two groups in the proportion of patients who completed bypass surgery, the proportion of middle meningeal artery retained, the postoperative patency rate, the proportion of temporary dysfunction, and the proportion of serious complications (P>0.05). Conclusion TOF-MRA sequence combined with navigation technology can effectively guide the surgical scheme design and postoperative evaluation of moyamoya disease.