Objective: In order to improve the accuracy and safety of screw implantation in the thin thoracolumbar pedicle, three-dimensional real-time navigation system was used.Methods: From 2016 to March 2019, 62 patients with thin thoracolumbar pedicle and spinal diseases were treated with intraoperative three-dimensional real-time navigation, including 22 males and 40 females, aged 19-65 years, with an average age of 42 years. There were 18 thoracic fractures, 35 lumbar fractures and 9 spinal deformities. At random, one side of the pedicle screw was implanted with navigation assistance (auxiliary group) and the other side was implanted with bare hand (unarmed group). After operation, the accuracy of pedicle screw implantation was evaluated by using thoracolumbar X-ray and CT plain scan, and referring to the Abul kasimhierarchy classification system.Results: There were 204 screws and 62 thoracic screws in 62 patients. The excellent and good rate of the auxiliary group was 93.5% (29 / 31), which was significantly better than that of the bare handed group (77.4%) (P < 0.05). The excellent and good rate of the auxiliary group was 97.2% (69 / 71), which was significantly better than that of the unarmed group (80.3% (57 / 71), the difference was statistically significant (P < 0.05).Conclusion: The application of intraoperative three-dimensional real-time navigation system in the operation of thoracolumbar thin pedicle screw implantation greatly improves the accuracy and safety of screw implantation.