Intestinal microbiota (IM) refers to the microorganisms present in the intestine, which are mediators that affect host‘s energy metabolism. The bioactive substances produced by them serve as a bridge between the IM and the host. The IM participates in various important physiological functions of the host, and is therefore closely related to the occurrence and development of numerous diseases. Both in terms of anatomical structure and function, the viscera are closely related to the intestine. This paper mainly discusses the research progress on the relationship between IM and its metabolites and related diseases of the viscera through literature research, and therefore, providing reference for disease diagnosis and treatment from the perspective of IM.