Inflammatory bowel disease ( IBD) is an autoimmune chronic inflammatory disease of unknown etiology. An abnormality in the intestinal mucosal immune system is a major factor in the development of IBD. Mesenchymal stem cells (MSC) have a self-renewal capacity and multipotent differentiation potential, which makes them important for the treatment of various diseases. Increasingly more researchers believe that the immunomodulatory function of MSCs is essential for the treatment of IBD. Upon tissue injury, MSCs improve the inflammatory microenvironment by regulating the immune response, which plays an important role in the process of tissue repair. This article mainly summarizes the research progress of MSCs in the treatment of IBD through immunomodulatory mechanisms.