Dental implants have been extensively used in prosthetic dentistry over the last two decades. Clinical experience shows that the healing and osseointegration process can heavily influence the success of the implantation. It is critical to understand the damage extent in different time frames. This paper aims at exploring the mechanical damage of dental implantation over the healing process. The 3D finite element analysis (FEA) models were developed based on computerised tomography (CT) scan technology to investigate the load-induced damage of interfacial osseointegration, as well as cortical and cancellous bone tissues. Unlike the existing linear finite element (FE) stress analysis, this study takes into account the damage accumulation and micro-crack nucleation under a framework of bone/interface remodelling. This study reveals the damage in the surrounding bone tissues and bone-implant interfaces at different stages of the healing process, and consequently premature load tolerances are suggested.