Fecal microbiota transplantation (FMT) is an innovative method to reconstruct the intestinal microecological balance by transplanting the fecal microbiota of healthy donors into patients, which provides help for the treatment of diseases. It has a good effect on the treatment of recurrent Clostridioides difficile infection (rCDI), and its therapeutic potential is not only limited to gastrointestinal diseases, but also can be continuously explored in other microbial-related diseases. In the exploration of factors for the success of FMT in the treatment of diseases, in addition to the recovery of intestinal bacteria, the regulation of intestinal phages is also involved. Intestinal phages, an important part of the gut microbiota, play an important role in the complex dynamics of bacteria; their transfer may be related to the curative effect of FMT. This review analyzed the biological characteristics of intestinal phage and the main bioinformatics analysis strategies, summarized the clinical research on the role of intestinal phage in FMT, explored the changes in the intestinal phage community in FMT and the possible mechanisms of action, and discussed the relationship between intestinal phage and the efficacy of FMT, as well as the existing safety issues. It can not only improve the understanding of the role of intestinal phages in FMT, but also promote the clinical application of FMT.