Abstract: Objective To evaluate the application effect and technical advantages of intraoperative CT navigation system in the process of insertion of pedicle screws during spinal deformity operation. Methods Clinical data about 60 cases who underwent spinal deformity surgery and were assisted by Siemens intraoperative slide 40 row CT scanning and Brainlab navigation system to insert pedicle screws in Chinese PLA General Hospital from January 2010 to January 2014, including 27 males and 33 females with an average age of 18.4 years (range from 11-38 years), were retrospectively analyzed. Results 650 pedicle screws were inserted in 60 cases, including 570 thoracic pedicle screws (12 screws were modified) and 80 lumbar pedicle screws (none was modified). The total, thoracic and lumbar accuracy of the placement of pedicle screws were 98.14%, 97.89% and 100%, respectively. Conclusion The intraoperative CT navigation system can display the form of thoracic and lumbar pedicle and the organization in front of the pedicle, and it can also precisely display the enter point and the angle of screw by three-dimensional imaging modules with low failure probability of pedicle and wall, low incidence of spinal cord injury and good application prospect.