Objective To investigate the feasibility of absorbable magnesium alloy screws in atlantoaxial dislocation fixation. Methods Four kinds of screws with triangular, rectangular, trapezoidal and zigzag thread were designed with WE43 magnesium alloy. The finite element simulation analyses were performed on the screw- polyurethane model and atlantoaxial fixation system model. The stress and displacement distributions on the models were obtained. Results The pull-out force simulations were carried out on four kinds of magnesium alloy screws according to ASTM F543 standard specification. The stresses of screws with triangular, rectangular, trapezoidal and zigzag thread were 146.20, 185.22,194.98, 264.55 MPa, respectively. The pull-out strength of the screw with triangular thread was the largest, and the peak stress was the smallest. The magnesium alloy screw with triangular thread used for atlantoaxial fixation could meet the strength requirements of flexion/extension, rotation and bending of the neck. The peak stress of the screw was reduced by 17.16 MPa after adding hydroxyapatite (HA) coating on the surface, and the stress on the screw was within the range of bonding strength between coating and magnesium alloy substrate. Conclusions Under the same loading condition, the screw with triangular thread has good stability and the best pull-out force performance. After heat treatment, the strength of magnesium alloy screw with triangular thread meets the load-bearing requirements for atlantoaxial dislocation fixation. HA coating on screw surface can optimize mechanical properties of the screw, and there exits good bonding strength between the coating and the screw.