Chronic fatigue syndrome(CFS)is a neuroimmune disease characterized by unexplained fatigue for a long time and ina-bility to recover energy after sleep.As a key factor regulating the central nervous system,intestinal flora participates in the occur-rence and development of CFS.To clarify the mechanism of intestinal flora in the pathogenesis of CFS,this paper analyzed the intes-tinal flora and its metabolites affecting CFS based on the microorganism-gut-brain axis,and discussed the internal mechanism of in-testinal flora imbalance in weakening endotoxin tolerance,destroying intestinal barrier,changing intestinal flora metabolism to regu-late the central nervous system of CFS.The paper facilitates the further research on intestinal microorganisms of CFS patients and provide a new clinical idea for the prevention and treatment of CFS.