Fecal microbiota transplantation (FMT) is a therapeutic approach that targets intestinal microorganisms by transplanting fecal microorganisms from healthy individuals into the gastrointestinal tract of diseased individuals, thus restoring the recipient ’ s disordered gastrointestinal microbiota by restructuring the intestinal flora. However, the mechanism of action and adverse effects of FMT in different diseases have not yet been clarified, thus limiting its wide clinical application. Its use still relies on in-depth preclinical studies; however, highly inconsistent or incomplete experimental details provided in current reports, coupled with a lack of authoritative standards and recommendations,seriously affect the interpretation of the study findings and replication of the experimental procedures, as well as hindering the clinical translation of the result. We therefore review and discuss the key steps of recipient selection and graft sample collection, storage, graft material preparation, and grafting route, with the aim of improving the utilization of experimental animals, consumables, and labor, and providing method ological recommendations and references to achieve replicability and standardization of preclinical FMT studies.