Abstract: The pathogenesis of autoimmune diseases is complex, and the therapeutic effects of traditional treatments on refractory autoimmune diseases are limited and unsatisfactory. Mesenchymal stem cells have been used in the treatment of diseases such as autoimmune diseases, graft-versus-host diseases and diabetes due to their strong immunomodulatory properties. This review summarizes the progress in the immunomodulatory mechanisms of mesenchymal stem cells, the pre-clinical study of mesenchymal stem cell transplantation and its clinical application in the treament of autoimmune diseases.