Abstract: Autoimmune diseases are characterized as the destruction of self-tolerance, abnormal activation of immune cells, production of autoantibodies and the release of large amounts of inflammatory factors, which in turn result in multisystem damage. The gut microbiota balance is closely related to the host health.Dysbiosis of gut microbiota has been identified in relation to many autoimmune diseases, including rheumatoid arthritis ulcerative colitis and autoimmune thyroiditis, etc. There has strong relationship between Chinese herbal medicine and its ability to alter the composition of the gut microbiota, and many studies has been proved that Chinese herbal medicine has therapeutic effect by reshaping the intestinal micro-ecological structure. In this review, we aim to investigate how gut microbiota affects the occurrence and development of autoimmune diseases, and to correlate the effects of Chinese herbal medicine on the regulation of gut microbiota with its effectiveness in disease prevention and treatment, with a view to providing a certain reference basis for the clinical application and pharmacological research of Chinese herbal medicine.