The gut microbiota plays an important role in the occurrence and development of many metabolic diseases, such as obesity, type 2 diabetes, non-alcoholic fatty liver disease and cardiovascular diseases. The gut microbiota can further metabolize bile acids synthesized in the liver and secreted into the gut to form secondary bile acids. A variety of bile acids form bile acid pools in different proportions, and target host bile acid receptors the Farnesoid X receptor and the G protein-coupled bile acid receptor, thereby affecting the metabolism of the host. This article reviews the ways in which the gut microbiota metabolizes bile acids and the mechanisms by which dynamic gut microbiota and bile acid pools regulate the progression of metabolic diseases.