The ocular surface microbiota is a part of the human ocular surface microenvironment and is critical to its stability. Many studies have explored the composition of the ocular surface microbiota in health and disease, but the research results are different based on internal and external factors, and the relationship between microorganism dysbiosis and diseases also remains unclear. As the research on intestinal microorganisms and systemic diseases has intensified in recent years, ophthalmic researchers have been inspired to further explore the relationship between ocular surface microbiota and non-infectious ocular surface diseases. Therefore, this article will review the core microbiota of the normal ocular surface as well as alterations in ocular surface microbiota in ocular and systemic diseases, and discuss the possible mechanisms of diseases caused by microorganism dysbiosis, hoping to provide a reference for future studies in ocular surface microbiota.