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Objective: Accurately inserting pedicle screws is the key point of posterior pedicle screw fixation for lower cervical spine (C3–C7) instability. 3D printing technology can improve the accuracy of screw placement. This study compared the safety of 3D‐printed flexible drill guiding template vs. traditional rigid drill guiding template for lower cervical pedicle screw insertion. Methods: This was a retrospective study. A total of 34 patients who underwent lower cervical pedicle screw fixation from March 2018 to May 2021 were enrolled in this study, and they were divided into the flexible drill flexible drill group and the traditional drill group. A total of 18 patients in the flexible drill flexible drill group underwent pedicle screw fixation assisted by 3D printed flexible drill guiding templates for the lower cervix, and 16 patients in the traditional drill group underwent pedicle screw fixation assisted by 3D printed regular drill guiding templates for the lower cervix. The length of the incision and intraoperative blood loss during surgery were recorded and compared for the two groups. The grade, deviation of the screw entry point, deviation of the screw medial angle and screw length were measured and compared after surgery for the two groups by independent‐sample tests. Results: There was a significant difference in the length of the incision and blood loss between the two groups (P < 0.05). There was a significant difference between the two groups for grade (P = 0.016). The deviation of the screw entry point was 0.65 ± 0.50 mm in the flexible drill group and 0.78 ± 0.83 mm in the traditional drill group. The deviation of the screw medial angle was 2.14 ± 1.78 in the flexible drill group and 4.23 ± 2.51 in the traditional drill group, with a significant difference between the two groups (P < 0.05). Conclusion: Compared with regular guiding techniques, lower cervical pedicle screw placement assisted by multistep navigation templates and flexible K‐wires results in less trauma and better safety. [ABSTRACT FROM AUTHOR]