Argon ion beam polishing technique was applied to prepare the cross sections of implants feasible for high resolution scanning electron microscope investigation. The interfacial microstructure between newly formed bone and implants with three modified surfaces retrieved after in vivo test using three different animal models was characterized. By this approach it has become possible to directly observe early bone formation, the increase of bone density, and the evolution of bone structure. The two bone growth mechanisms, distant osteogenesis and contact osteogenesis, can also be distinguished. These direct observations give, at microscopic level, a better view of osseointegration and expound the functional mechanisms of various implant surfaces for osseointegration.