In recent years, the pathogenesis of "gut-liver axis" in alcoholic and nonalcoholic fatty liver disease has attracted more attention in this field. In this paper, the relationship among fatty liver, gut-permeability, gut-derived endotoxin, and gut microbiota was systematically clarified. Based on the researches of treatment and prevention of fatty liver and gut injury by Chinese medicine, the gut is believed as the curative target for fatty liver disease, which not only is the modern annotation for the Chinese medicine practice, but also might possibly become an important view angle and strategy for fatty liver disease treatment.