Metabolic diseases have shown a global trend of high prevalence in recent years, causing a heavy social burden. In Chinese medical theory, the spleen is responsible for transporting water and grain throughout the whole body. The dysfunction of the spleen in transportation would affect the fluidity of the human body, resulting in phlegm and dampness, eventually leading to metabolic disturbance. However, the microscopic mechanism of the above phenomenon remains unclear. Intestinal homeostasis refers to the dynamic state of equilibrium formed by the interaction between the host mucosal barrier and the intestinal microecology. The factors such as intestinal flora and its metabolites, intestinal barrier, intestinal mucosal immunity and the host intestinal function are involved. According to the theory of visceral manifestations, the intestinal tract belongs to the spleen category in traditional Chinese medicine, and the destruction of intestinal homeostasis is closely related to metabolic diseases. This article proposes that the “intestinal origin theory”of metabolic diseases could provide a new scientific interpretation of the traditional Chinese medicine theory of spleen dysfunction in transportation, explain its scientific connotation and provide a novel intervention target for the prevention and treatment of metabolic diseases by traditional Chinese medicine.