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Crohn’s disease which mainly affects the gastrointestinal tract and impairs patient’s quality of life, is a refractory inflammatory disease with clinical manifestations of abdominal pain, fever, bowel obstruction and diarrhoea with blood or mucus. Besides the common complication of intestinal obstruction, the formation of fistulas should also be concerned about and anorectal fistula is the most typical. The disease is difficult to radical cure and easy to relapse, which urges people to find other effective treatment in addition to surgery. Given the challenges and prospective medical needs in Crohn’s fistula, attention has been directed at stem cell therapy. Several studies suggest that mesenchymal stem cells (MSCs) improve Crohn’s disease and Crohn’s fistula. In the recent years, a lot of studies of mesenchymal stem cell transplantation or local rejection with bone marrow-derived stem cells and adipose tissue-derived stem cells have been reported in the treatment of refractory Crohn’s disease and many of which are in remission. A number of clinical trials for refractory Crohn’s disease have also evaluated autologous or allogenic MSCs and have shown that MSCs can be safely administered with some patients achieving clinical response.