Objective To investigate the application value of intraoperative CT navigation in posterior thoracic pedicle screw placement for scoliosis patients. Methods Between October 2009 and December 2011, 46 patients with scoliosis were treated with thoracic pedicle screw placement under intraoperative CT navigation in 21 cases (group A) or under C-arm fluoroscopy in 25 cases (group B). There was no significant difference in age, gender, type of scoliosis, involved segment, and Cobb angle of main thoracic curve between 2 groups (P gt; 0.05). A total of 273 thoracic pedicle screws were placed in group A and 308 screws in group B. The pedicle screw position evaluated and classified by intraoperative CT images according to the Modi et al. method; and the accurate rate, the safe rate, and the potential risk rate of pedicle screws were calculated on the upper thoracic spine (T1-4), the middle thoracic spine (T5-8), the lower thoracic spine (T9-12), and the entire thoracic spine (T1-12). The accuracy and security of thoracic pedicle screw placement were compared between 2 groups. Results On the entire thoracic spine, the accurate rate of group A (93.4%) was significantly higher than that of group B (83.8%), the safe rate of group A (98.9%) was significantly higher than that of group B (92.5%), showing significant differences between 2 groups (P lt; 0.05). However, the potential risk rate of group B (7.5%) was significantly higher than that of group A (1.1%) (P lt; 0.05). On the upper, the middle, and the lower thoracic spines, there was no significant difference in the accurate rate, the safe rate, and the potential risk rate of pedicle screws between 2 groups (P gt; 0.05). According to CT evaluation results, the potential risk pedicle screws were revised or removed during operation. The patients of 2 groups had no neurological deficits through physical examination of nervous system at 3 days after operation. Conclusion Intraoperative CT navigation can improve the accuracy and security of posterior thoracic pedicle screw placement and it can ensure the safety of operation by finding and promptly removing or revising the potential risk pedicle screws.