Fecal Microbiota Transplantation (FMT) is a therapeutic method that transplanted microorganisms from healthy donors' feces into the gastrointestinal tract of patients to directly change the intestinal microbiota of patients, normalize its composition, and achieve therapeutic effects. Chronic diarrhea is closely associated with gut microbiota. The imbalance of gut microbiota can lead to the occurrence and progression of chronic diarrhea. FMT is a crucial and effective approach for the treatment of chronic diarrhea. This review aims to summarize the relationship between chronic diarrhea and gut microbiota, as well as the research advancements and applications of FMT technology in managing chronic diarrhea, while also addressing prevailing challenges and future prospects. It aims to provide a reference for further study of FMT in the treatment of chronic diarrhea.