OBJECTIVES: Traditional cortical bone trajectory (CBT) screws in the lumbar spine offer greater holding strength and are well-suited for patients with osteoporosis. However, the screw implantation procedure is challenging and associated with significant risk. This study aimed to assess whether individualized 3D-printing navigation technology provides higher accuracy and better clinical outcomes compared to the free-hand isthmus method for lumbar CBT screw implantation. METHODS: From September 2020 to August 2023, a total of 41 patients who underwent CBT screw surgery were retrospectively collected. Among them, 23 patients underwent the free-hand isthmus method (Group A), while 18 patients underwent the individualized 3D-printing navigation technique (Group B). All imaging and clinical data for these patients were collected in a blinded manner. RESULTS: During the surgery, 185 CBT screws were implanted into the lumbar spines of 41 patients-78 in Group A and 107 in Group B. After the surgery, the majority of implanted screws (86.5%) were classified as grade 0, indicating satisfactory implantation. Compared to Group A, Group B had fewer screws classified as grade 1 or grade 2 ( = 0.045), indicating higher accuracy in screw implantation. Additionally, Group B also had a shorter operation duration ( = 0.02), fewer fluoroscopy exposures ( < 0.01), and less blood loss ( = 0.03). In addition, compared to Group A, individuals in Group B showed significant improvement in back pain symptoms at both 3 and 6 months ( = 0.01 and <0.01), as well as in physical activity at 3 months ( = 0.02) postoperatively. No significant difference in postoperative complications was observed between the two groups. CONCLUSION: Compared to the free-hand isthmus method, lumbar CBT screw implantation with individualized 3D-printing navigation technology shows higher accuracy, shorter operative time, reduced intraoperative fluoroscopy and blood loss, and better clinical outcomes at three months post-surgery.