Bile acids are a class of cholesterol derivatives that play important roles in cholesterol and energy homeostasis and intestinal nutrition absorption. Bile acids are mainly synthesized in the liver. During fasting, bile acids are secreted from the liver and stored in the gallbladder. After a meal, the stored bile acids are released into small intestines. In the intestine, about 95% of bile acids will be re-absorbed and travel back into the liver through port veins, which is called bile acid enterohepatic circulation. This enterohepatic circulation of bile acids plays important roles in the emulsification and intestinal absorption of lipids and other nutrition. On the other hand, bile acids function as ligands for a number of receptors, such as farnesoid X receptor (FXR), proterane X receptor (PXR), vitamin D receptor (VDR) and cell membrane surface receptor-G protein coupled receptor (TGR5), which play important roles from metabolic homeostasis to innate immunity. A number of cytokines such as hepatocyte growth factor (HGF), interleukin-1β (IL-1β) and tumor necrosis factor α (TNF-α) regulate the homeostasis of bile acids. In the current review, we will summarize the recent progress in the regulation of bile acid synthesis and its physiological and pathological functions from energy homeostasis to innate immunity and cancer progression to provide a reference for the study of bile acid metabolism.