Objective To study the change patterns of bone microstructural parameters around the magnesium based- implants after implantation in rabbit femur at different implantation time points. Methods The threaded and non-threaded high-purity magnesium (HP Mg, 99.99 wt.%) screws, with a 2 mm diameter and a 7 mm length, were implanted into the femoral condyle of the rabbits. The control group was the drilled and healthy group. Micro-CT scanning and analysis were performed at 8th, 12th and 16th week after operation. The obtained microstructural parameters included bone mineral density (BMD), bone volume fraction (BV/TV), trabecular thickness (Tb.Th), trabecular number (Tb.N), trabecular separation (Tb.Sp). Results At 8th week, BMD and BV/TV in non-threaded magnesium screw group were significantly higher than those in healthy group, Tb.N was significantly higher than that in drilled and healthy group, and Tb.Sp was significantly lower than that in healthy group. At 12th week, BMD, BV/TV and Tb.N in threaded magnesium screw group were significantly higher than those in drilled and healthy group, Tb.Th was significantly higher than that in healthy group, and Tb.Sp was significantly lower than that in drilled and healthy group. At 16th week, BMD, BV/TV and Tb.N in non-threaded magnesium screw group were significantly higher than those in drilled and healthy group, and Tb.Sp was significantly lower than that in drilled and healthy group. Conclusions The magnesium based-implant promoted higher BMD, BV/TV, Tb.Th, Tb.N and lower Tb.Sp of surrounding implant, indicating that osseointegration and bone growth were in good condition. Magnesium based-implant could effectively promote the regeneration of bone. The results provide a theoretical basis for the orthopedic application of magnesium based-implants in clinic.