Background: Cubitus varus deformity is a common sequela of elbow fractures in children. Cubitus varus deformity treatment is tending toward 3D correction, which is challenging for orthopedic surgeons. This study aims to explore whether individualized 3D-printed navigation templates can assist with accurate and effective corrective treatment of children with cubitus varus deformity. Methods: Thirty-five patients were treated for cubitus varus deformity from June 2015 to April 2017, including 21 boys and 14 girls, aged 4.6-13.2 years (average, 7.5 years). Of these cases, 17 deformities were on the left side and 18 were on the right side. All were treated with wedge osteotomy of the lateral distal humerus. 3D-printed navigation templates were used in 16 cases, while traditional surgery was used in 19 cases. All patients underwent computed tomography scans before surgery. Computer software was used to analyze the measurements and design and print individualized navigation templates. The navigation templates were matched, and surgery was initially simulated. Intraoperative individualized navigation templates were used to assist with accurate osteotomy and Kirschner wire fixation. Operation times were recorded in all cases, the carrying angles before and after surgery were assessed by computer, and postoperative elbow joint function was evaluated using Bellemore criteria. All measurement data were presented as means ± SD, and Student's t test was used to examine differences between groups. All count data between both groups were compared using the chi-square test or Fisher's exact test analysis. Results: All individualized navigation templates matched well with the corresponding anatomical markers and were consistent with preoperative planning, simulated surgery, and intraoperative procedures. Average operation times from clear exposure to fixed Kirschner wire were 11.69 min (9.6-13.5 min) for the individualized navigation template group and 22.89 min (17.7-26.8 min) for the traditional operation group (p < 0.001). Average differences in postoperation carrying angles between affected and healthy sides were 1.13°(0-2.0°) and 4.21°(0-7.5°), respectively (p < 0.001). Follow-up 6-12 months postoperation showed that elbow function did not differ significantly between groups using the Bellemore criteria (p > 0.05). Conclusions: Individualized navigation templates simplify procedures, reduce operation time, and improve accuracy when used in orthopedic surgery to treat children with cubitus varus deformity.