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Magnesium (Mg) has been widely accepted as osteoconductive biomaterial, but osseointegration of Mg device at different implantation sites is still unclear. In the present study, high-purity magnesium (HP Mg) pins were implanted into femoral shaft and condyle of New Zealand rabbits concurrently. 2, 8, 12 and 16 weeks after surgery, rabbit femurs were harvested for micro-computed tomography (micro-CT) scanning and subsequent histological examinations. HP Mg pins were retrieved for scanning electron microscope and energy dispersive spectrum (SEM/EDS) analyses. HP Mg pins at both implantation sites performed stable corrosion with mineral deposition and bone incorporation on surface. However, difference in distribution of contact osteogenesis centers and biological properties of peri-implant bone tissues was detected between femoral shaft and femoral condyle. In femoral condyle, contact osteogenesis centers originated from both periosteum and cancellous bones and the whole HP Mg pin was encapsuled in trabecular bone at 16 weeks. Meanwhile, bone volume to total bone volume (BV/TV) and bone mineral density (BMD) of peri-implant bone tissues were above those of normal bone tissues. In femoral shaft, contact osteogenesis centers were only from periosteum and direct bone contact was confined in cortical bone, while BV/TV and BMD kept lower than normal. Furthermore, new formation of peri-implant bone tissues was more active in femoral condyle than in femoral shaft at 16 weeks. Therefore, although HP Mg performed good biocompatibility and corrosion behavior in vivo, its bioadaption of osseointegration at different implantations sites should be taken into consideration. Bone metaphysic was suitable for Mg devices where peri-implant bone tissues regenerated rapidly and the biological properties were close to normal bone tissues.