Two-stage implant systems are currently adopted in most implant prostheses. However, an implantabutment microgap inevitably forms because of masticatory load under physiological function, manufacturing errors, and micromotion. More alveolar bone is absorbed when a deep microgap forms in the jaw. Additionally, less bone is resorbed around the necks of implants in the internal connection systems than in the external, as well as in the conical internal connection systems than in the butt joint connection systems. Less bone is also resorbed when the implants and the abutments are highly compatible. Platform switching technology can effectively reduce alveolar bone absorption around the necks of implants. Implant-abutment microgaps mainly affect the bones around the necks of implants via micromotion and microleakage, including bacterial and molecular leakages. Bacteria and small molecules enter the interior of the implants through the microgaps, settle and breed, and then become an infection focus of the peri-implantitis. Micromotion generates local stress and promotes microleakage. To preserve the alveolar bone around the necks of implants, we should select the equicrestal or supercrestal implant depth for the butt joint connection systems and the subcrestal implant depth for the conical internal connection systems, use the internal connection systems and implant systems, which offer good compatibility, and then apply the platform switching technology reasonably. This study aims to summarize the effect of implant-abutment microgap on the bone surrounding the necks of implants, including its mechanism.