Objective: To investigate the efficacy of microscope-assisted free-hand atlantal pedicle screw technique for unstable atlas burst fracture. Methods: A retrospective case control study was conducted to analyze the clinical data of 48 patients with unstable atlas burst fracture admitted to Ningbo No.6 hospital from January 2016 to June 2018. There were 32 males and 16 females, aged 24-72 years [(49.5±15.2 years)]. A total of 22 patients were treated with the technique of atlas screw placement by drill under microscope (Group A), including 14 males and eight females, aged 24-68 years. Twenty six patients (Group B) were treated with atlantal pedicle screw placement by hand, including 18 males and 8 females, aged 26-72 years [(50.7±15.4 years)]. The operation time, intraoperative blood loss and the times of intraoperative fluoroscopy were compared between the two groups. X-ray and CT were reexamined to evaluate the accuracy of screw placement within one week after operation. The visual analogue score (VAS) and cervical dysfunction index (NDI) were compared before operation and 1 year after operation. The intraoperative complications were recorded. One year after operation, X-ray and CT were reexamined to observe fracture healing, atlantoaxial fusion and failure of internal fixation. Results: Group A was followed up for 12-24 months [(18.4±6.8)months], and Group B for 12-24 months [(17.4±7.2)months]. The amount of intraoperative bleeding [(180.5±60.8) ml] and the times of intraoperative fluoroscopy [(1.3±0.8) times] in Group A were significantly lower than those in Group B [(280.1±80.2) ml, (2.2±0.8) times] (P<0.05), but there was no significant difference in the time of operation and the accuracy of screw placement (P>0.05). There were statistically significant differences in VAS and NDI before operation and one year after operation in both groups (P<0.05), but there was no significant difference between the two groups (P>0.05). No serious complications such as vertebral artery, nerve root and spinal cord injury occurred. One year follow-up CT showed healed fracture or continuous bone bridge passing through the atlantoaxial intervertebral space. Except for one patient in Group B with lost reduction, other patients had no loosening or fracture of internal fixation. Conclusion Compared with screw placement by hand, the pedicle screw placement by drill under the microscope can reduce the amount of bleeding and the times of fluoroscopy.