[Objective] To investigate the changes of the rotation of the vertebral body between preoperative supine position by MRI scans and intraoperative prone position O-arm system scans in adolescent idiopathic scoliosis. [Methods] A retrospective study was conducted on 21 AIS patients who underwent posterior incision and internal fixation from April 2013 to July 2018 in the orthopedic department of the medical center. All patients underwent the full spine MRI scans of preoperative supine position and the O-arm system scans of the intraoperative prone position. Using the G??en method to measure the angles of rotation of the same vertebral body for every patient about preoperative MRI and intraoperative O-arm scans including the rotation of the main thoracic vertebrae (AVR), the upper end vertebra (UEVR), the lower end vertebra (LEVR), adjacent vertebrae above UEV (AVAUEVR) and adjacent vertebrae below LEV rotation (AVBLEVR). The difference in rotation under different body positions of the vertebral body was compared by the paired t-test. [Results] The degree of rotation of apical vertebrae(AVR) in the supine position in the main thoracic vertebrae was significantly greater than the degree in the prone position (the conventional posterior surgical position). The mean difference was 3.14°. And the difference was statistically significant (P=0.015, <0.05). In the prone position, the UEVR and AVAUEVR degrees were increased by comparing with the supine position. The average difference was 1.98° and 0.83°. The prone position LEVR and AVBLEVR degrees were reduced by comparing with the supine position, and the average difference was 1.07° and 1.86°, but there was no significant difference in the degree of UEVR, LEVR, AVAUEVR, and AVBLEVR between the two positions (P>0.05). [Conclusion] The O-arm navigation system can be used to obtain the axial images of the vertebral body. The rotation of the vertebral body can visually be observed. At the same time, it can be observed for the rotation of the vertebral body before and after the placement of the screws. It is an important clinical surgical aid.