Metagenome refers to the sum of genetic material of all the microorganisms in an environment. The technology of metagenomics can make the best use of microbial resources in the environment, which has attracted increasing attention of microbiological researchers at home and abroad. There is a large number of microorganisms in the oral cavity, and the available studies about the microorganisms causing oral diseases are mostly limited to bacterial culture method. However, some microorganisms are difficult or unable to be cultured. Metagenomics technology will break this limitation and help to explore more oral microbial resources. Recent studies based on metagenomic sequencing have mapped the oral ecosystem, and more and more experiments have proved the role of oral microbiome in oral diseases and even systemic diseases. At the same time, these studies pave a new way for the diagnosis and treatment based on human microbiome. This review demonstrates that metagenomics is a powerful tool for the study of microorganisms related to human oral diseases and systemic diseases and has a broad development prospect, and also discusses the limitations to be overcome in the application of metagenomics.