Fecal microbiota transplantation (FMT) has become an important method for treating various diseases. This review explores the relationship between FMT and various diseases such as inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), metabolic disorders, neurological disorders, tumors, and cardiovascular diseases, and analyzes the key mechanisms by which FMT exerts therapeutic effects. The mechanism of FMT involves signaling pathways such as Toll-like receptor 4 (TLR4)/NF-κB pathway, Aryl hydrocarbon receptor (AHR) pathway, NLR family pyrin domain containing 3 (NLRP3) inflammasome pathway, short chain fatty acid (SCFAs)-mediated pathway, and 5-hydroxytryptamine pathway. These pathways alleviate disease symptoms by synergistically regulating immune responses, inflammatory processes, and metabolic functions. In addition, this review also discusses different administration methods of FMT, including traditional colonoscopy or enema administration, oral FMT capsules, nasogastric/nasoduodenal tube administration, and rectal administration for pediatric patients. Although there are still technical and clinical challenges, FMT, as an individualized treatment strategy, has shown broad application prospects in the treatment of various diseases.