Abstract: The gut microbiota and their metabolites play a critical role in the maintenance of host immune homeostasis. The dysbiosis and gut microbiota-derived metabolites are closely associated with the initiation and development of multiple autoimmune diseases. Among the microbiota metabolites, short-chain fatty acids, tryptophan and its derivatives, and bile acids are the most widely studied. In this review, the metabolic pathway of the microbiota metabolites, their functions in the immune response and the current findings on their correlation with autoimmune diseases are summarized, with the hope of revealing the role of gut microbiota-derived metabolites on the pathogenesis of autoimmune diseases.