Objective To design a nailing guiding device to improve individual atlas pedicle screw implantation, avoiding the damage of adjacent tissues and reducing the risk of operation. Methods Three-dimensional data of CT scan of 30 adult atlas were collected and analyzed by SPSS 21.0 software with 95% reference value range. The height of the posterior arch in starting point, the horizontal distance between starting point and the center of posterior tubercle, and the longitudinal distance from starting point to cortical bone of anterior arch through the center of lateral mass were determined for designing the guiding device. The designing steps included:(1) the fixing device of guider was designed with posterior tubercle of atlas as the anchor point; (2) based on the anchor point, vertical lifting rod and lateral vernier stents were installed to resist the external force of nailing and to preliminarily locate the starting point refering to the preoperative imaging data, repectively; (3) a needle sleeve was installed on the transverse stents, and the position of starting point and the direction of screw were determined; and (4) other parts included 2 mm diameter needle, screw nut, screw driver, etc. Clinical study:the designed guider was used in patients with atlanto-axial dislocation or instability, and patients receiving tranditional therapy were taken controls. The efficay of designed guider was evaluated by comparing the success rates and operation time of the two methods. Results The nailing success rate of the designed guider was significantly higher than that of the control group (96.15%[25/26] vs 84.61%[22/26], P=0.025). The Operation time of the guider group was significantly shorter than that of control group ([123.38±5.59] vs[137.62±4.15] min, P<0.05). Conclusion We have successfully designed an individual guiding device for atlas pedicle screw implantation, which can help to improve the operation efficiency.