Objective To compare the in vivo degradation rates of two different kinds of high purity magnesium bone screws by animal experiments, so as to make some suggestions on structural design of high purity magnesium bone screws. Methods High purity magnesium bone screws with threads and without threads were implanted into femoral condyles of New Zealand rabbits separately. Twenty-four rabbits were randomly divided into 3 groups. They were euthanized at 8, 12 and 16 weeks after operation, respectively. The in vivo degradation rates of bone screws with two different shapes were compared through micro-CT scanning and Skyscan CT-analyser software, and the stress changes during the progress of bone screw degradation were analyzed. Results The initial surface area of threaded screws ［(31.70±0.06) mm2］ was significantly greater than that of the non-threaded ones ［(29.56±0.22) mm2］. After 8, 12 and 16 weeks, the volume loss ratios of the threaded screws were (26.01±3.44)%, (33.35±5.05)%, (36.84±6.99)%, respectively, and the volume loss ratios of the non-threaded screws were (22.53±4.78)%, (31.12±6.59)%, (43.22±9.31)%, respectively. At the same time point, there were no significant differences in the volume loss ratio between two kinds of screws. The relationship between the volume reduction and the implantation time was linear for non-threaded screws and gradually decreasing for threaded screws. Conclusions Under the low-bearing condition, different structural design for high purity magnesium screws has no obvious effect on their degradation rate in vivo.