Inflammatory bowel disease （IBD） is a group of chronic non-specific diseases characterized by intestinal inflammation and mucosal damage，including ulcerative colitis （UC） and Crohn's disease （CD）. The etiology of IBD is complex，and the pathogenesis has not yet been fully clarified. However，it is generally believed that the interaction among genetic，environmental，immune and other factors are the main reasons for the occurrence and development of IBD. With the deepening of research，it is found that intestinal flora dysbiosis and intestinal mucosal barrier damage also play an important role in the progress of IBD. The conventional medical treatment of IBD often has limited efficacy and is prone to major adverse reactions. Therefore，in recent years，new treatment methods for IBD，including fecal microbiota transplantation （FMT），aimed at regulating intestinal microbiota，have attracted extensive attention. In this review，the pathogenesis of IBD，the importance of flora to organism，the relationship between the flora and IBD，the mechanism of FMT and the effectiveness and safety of FMT in the treatment of inflammatory bowel disease will be summarized，in an attempt to provide some reference for the individualized treatment of inflammatory bowel disease with FMT in the future.