Dental implantation is a routine treatment for tooth loss. With the increasing number of cases of planting failure, the main factor, peri-implantitis, has become the focus of experts and scholars. We recently found that certain systemic and local factors, such as smoking, drinking, diabetes, periodontitis, estrogen deficiency, oral hygiene, and cemented prostheses, may be involved in the occurrence, development, and prognosis of this disease. The Human Microbiome Project and other metagenomic projects worldwide have advanced our knowledge of the human oral microbiota, and the focus on the microbiology change of implants has gradually increased. We aimed to determine the influence of oral microbiota on the occurrence, development, and prognosis of peri-implant diseases by reviewing the recent research progress on peri-implant disease-related oral and systemic diseases.