Objective: To explore the clinical application effect of 3D printed guide and computer navigation-assisted pedicle screw placement in congenital scoliosis surgery. Methods: Fifty-five cases with congenital scoliosis treated from January 2015 to December 2019, were analyzed retrospectively. According to the pedicle screw placement method, the patients were divided into 3D printing group with 36 cases and navigation-assisted group with 19 cases. Data of perioperative period, clinical effect and other imaging data were compared in the two groups. Results: The operation of both groups of patients were successfully completed. The operation time, nail placement time, and intraoperative blood loss of 3D printing group were significantly less than that of the navigation group, which was statistically significant(P<0.05). The number of intraoperative fluoroscopy was more in 3D printing group(P<0.05), while there were no significant differences in incision length, precision nail placement rate, postoperative drainage volume, and hospital stay (P>0.05). The average follow up was 45.7±13.4 months and there was no significant difference in VAS score, ODI score and JOA score between the two groups at 1 month after operation, 6 months after operation and the last follow-up (P>0.05). In terms of imaging evaluation, there was no statistical difference (P>0.05) in coronal Cobb angle, local kyphotic Cobb angle, C7-S1 coronal deviation (C7-CSVL), sagittal deviation (C7-SSVL) of the two groups preoperatively, immediately after surgery and at the last follow-up. Conclusion: The 3D printed guide and the computer navigation-assisted method can both place pedicle screws accurately and correct the congenital spinal deformities. However, the 3D printed guide has more advantages in operation time, pedicle screw placement time, intraoperative blood loss and satisfaction.