Inflammatory bowel disease (IBD) is a chronic relapsing disease, including ulcerative colitis (UC) and Crohn's disease (CD). Although the etiology of IBD is unknown, but more and more evidence show that the inappropriate immune response to intestinal commensal bacteria leading to dysbiosis, and pathogens further act to the mucosal lymphoid tissue, causing IBD. Has yet not to determine the specific one or more pathogens as the cause of IBD,but literatures confirm the changes of diversity of the intestine flora.Based on the current awareness of changes in the intestinal flora in IBD, fecal microbiota transplantation (FMT) proposed in recent years to rebuild the intestine flora balance to achieve therapeutic purposes. But fecal bacteria of patients can not consistent with donor's for a long term after transplantation and therefore it is not an ideal way for disease control. Maintaining the diversity of flora in a long time so that well controlled the disease become the breakthrough of fecal microbiota transplantation in the treatment of inflammatory bowel disease.