In recent years, the probability of suffering from clostridium difficile infection (CDI) has increased significantly in clinical practice, and clostridium difficile began to have multiple drug resistance to antibacterials. A new treatment measure, fecal microbiota transplantation (FMT), can improve clinical symptoms in a short time of period and has shown great efficacy in the treatment of CDI. In addition, more and more researchers have tried to apply FMT in the treatment of inflammatory bowel disease, irritable bowel syndrome, metabolic syndrome and other diseases at home and abroad, and its clinical application needs to be further explored. At present, there are still problems unsolved in the aspects of the choice of the donor and the method of transplantation, and the security and validity of the transplant technology still need to be further studied. This paper introduced the development history, clinical application and operation flow of FMT.