The intestinal virome is an important component of the human intestinal microecosystem. In recent years, the relationship between intestinal microbiome and diseases has attracted extensive attention. More and more evidence has demonstrated that the transfer of intestinal virome in fecal microbiota transplantation is essential for the efficacy of the therapy. By reviewing the relevant studies in recent years, this article summarizes the therapeutic potential and possible mechanisms of intestinal virome in fecal microbiota transplantation, and makes an outlook on the application of intestinal virome in disease treatment.