Resistant starch is not easily digested and absorbed in the small intestine, but it can be utilized by the large intestinal microflora to produce metabolites such as short-chain fatty acids, which in turn can regulate the intestinal microfloral balance and bile acid metabolism. Therefore, this article puts forward the “resistant starch-intestinal flora-metabolite” nutrition axis to systematically summarize the mechanism of action by which RS mediates the production of metabolites by regulating the intestinal microflora. It compares the effects of intestinal microbial fermentation on the apparent, crystal and molecular structure of RS, describes the relationship of the structural characteristics of RS with the intestinal community structure, the production of short-chain fatty acids and the excretion of bile acids, and summarizes the mechanism of RS for improving metabolic diseases by regulating the intestinal microflora and intestinal metabolites. Besides, an outlook is given on future studies on the pathways of the interaction among resistant starch, the intestinal microflora and bile acid, and on the mechanism of RS interaction with bile acids and short-chain fatty acids in metabolic diseases.