In recent years, metagenomics(MGS)is the fastest growing fields in microbiology, and has been broadly applied in the detection of pathogenic microorganisms. Comparing with the traditional poly merase chain reaction(PCR)-based detecting technology which relies on microbial culture, MGS can directly detect the sequences of the total microbial DNA from uncultured samples with the high-throughput sequencing platform. It can help the doctors identify the involved pathogens more quickly and provide better medication guidance. Among the known ophthalmic diseases, a lot of them are caused by the infection of pathogens and have many difficulties in clinical diagnosis and treatment. The development of metagenomics provides us a more effective and reliable way for detecting the pathogens of ophthalmic diseases. This article was aimed to review the development of MGS, applications and in the field of ophthalmology, as well as its current deficiencies and the possible development directions in the future.