Intestinal Flora(IF)，which is called the largest endocrine organ in the body，produces a large number of bioactive metabolites which affect the physiological and pathological processes of the host.Studies have shown that some Traditional Chinese Medicine（TCM）can not only regulate probiotics or prebiotics，but also have the effect of probiotics and prebiotics.They can play a variety of biological effects through IF and treat related diseases by regulating the structure and function of IF.At the same time，intestinal flora may increase the efficacy or reduce the toxicity of TCM.The interaction mechanism involves reversal of TMAO，reduction of endotoxin，inhibition of colonization of pathogenic bacteria，increase of intestinal mucosa sIgA secretion，inhibition of-glycosidase activity，etc.In this paper，the mechanism of interactions between TCM and IF，and the use of IF to intervene in related diseases were discussed，so as to provide directions for future research.