Intestinal flora plays an important role in the process of resisting infectious diseases. Fecal microbiota transplantation (FMT) is an important method for reconstructing intestinal microbiota, mainly includes washed microbiota transplantation, transendoscopic enteral tubing, and spore group transplantation. In 2022, the Standardization Administration of China released the technical standards for Quality control of fecal microbiota washing and grading of fecal microbiota specimens, aiming to reduce adverse events related to FMT and improve the acceptance of FMT by patients and medical personnel. After the success of FMT in the treatment of recurrent Clostridioides difficile infection, its application in the treatment of other infectious diseases has also become a global research hotspot. This paper reviews the development of FMT and its application in various infectious diseases.