Background: Three-dimensional CT reconstruction of prone position could measure the relative position between the Great vessels and the thoracolumbar vertebrae. The Great vessels positions of the thoracic and lumbar segments were studied to improve the accuracy of pedicle screw insertion, reduce the risk of vascular injury. Methods: Twenty-four adults participated in the present study. Three-dimensional reconstruction of thoracolumbar (T9–L3) CT was performed in the prone and supine positions. The relative distance between the arteriovenous vessels and vertebrae distance (AVD/VVD) was obtained, respectively. The relative position angle of the arteriovenous vessel and the vertebral body was calculated as ∠AOY/∠VOY. Self-controlled experiments were carried out in the prone and supine positions. The data obtained were analyzed using SPSS 22.0 statistical software. Results: With regard to AVD, The AVD of the T12 was the smallest,> 3.2 mm. The difference among the T9, T10, L2 level was statistically significant (P < 0.05). And AVD was greater in the prone position than in the supine position; while the value of ∠AOY is the descending from T9-L3 gradually, there were statistically significant differences in ∠AOY between T9-T12, L2 and L3 in prone and supine position (P < 0.05). The aorta in the prone position was closer to the midline than that of the supine position, varying from 0°to 30°near the Y axis. With regard to VVD, there was no significant difference in contrast between the prone and supine positions (P≥0.05), and the VVD was the smallest in the L3 level> 5.4 mm. Conclusion: The pre-vertebral position of the aorta may change from T9 to L3 due to changes in body position. When the T9-L3 thoracolumbar spine disease was treated with pedicle screw double cortical fixation, the screw was safe and reliable within a range of≤ 3 mm when broken the pre-cortex .The three-dimensional reconstruction of prone position CT could be used to more accurately assess the relative position of the vertebral body and the blood vessel.