Various theories have been developed as to the etipathogenesis of inflammatory bowel disease (IBD), but so far none of them has led to a therapy with long-term efficacy and free of side effects. The modern hygienic lifestyle is probably at the foot of the disease where, in genetically susceptible hosts, the intestinal commensal flora triggers dysregulated immune and inflammatory responses. Current therapies from anti-inflammatory drugs to immunosuppressive regimens remain inadequate. With the development of research on stem cells, some progress has been achieved in the application of stem cell transplantation to the treatment of IBD. This article mainly introduces the application of mesenchymal stem cell(MSCs) transplantation to the treatment of IBD and the possible mechanism of this novel therapy.