The etiology of inflammatory bowel disease (IBD) is complex, and the mechanism has not yet been fully clarified. It is currently believed that the progression of the disease is related to the alterations of intestinal flora. Conventional medical anti-inflammatory treatment has large side effects. In recent years, with the continuous study of intestinal flora, a new kind of therapy has been applied to the disease. Many randomized controlled trials (RCT) of fecal microbiota transplantation (FMT) have achieved good therapeutic effects on IBD, and this regimen has received extensive attention. This paper reviews the progression of FMT and its mechanisms of intestinal function regulation in the past five years. Meanwhile, the challenges and future directions in the research of FMT are also summarized.