Objective To study anatomical and clinical effect of atlas pedicle screw implantation. Methods A total of 46 atlas sample were measured by crew from Department of Anatomy, Chengde Medical College for information of entry point and angle of pedicle screws. Totally 30 cases of control group who were admitted into our hospital from March 2013 to March 2015 underwent posterior atlantoaxial internal fixation by conventional pedicle screw way for treatment of atlantoaxial instability. Another 33 cases in experimental group who were admitted into our hospital during August 2015 to August 2017 underwent posterior atlantoaxial internal fixation with local anatomical landmarks for treatment of atlantoaxial instability. The operation indexes, ODI and JOA score before and after surgery, and postoperative complications were recorded in two groups. Results operation time, intraoperative blood loss and insertion time in experimental group were decreased significantly when compared with those in control group (P < 0.05). No obvious differences in ODI and JOA scores pre- and post-surgery were identified between groups (P > 0.05). ODI was decreased while JOA was increased post-surgery greatly in both groups when compared with that prior to surgery (P < 0.05). Conclusion Local anatomical landmarks is a promising pre-surgery evaluating system for atlas screw placement.