Congenital biliary tract malformations are a series of rare but extremely serious diseases that mainly include biliary atresia and biliary hypoplasia (referred to as Alagille syndrome). The rapid progression of biliary atresia and Alagille syndrome results in jaundice, cholestatic liver disease, cirrhosis, and even liver failure. In most cases, supportive or clinically specific therapies cannot achieve satisfactory outcomes. Therefore, liver transplantation (especially living donor liver transplantation) may be required. As many studies have elucidated the role of genetic factors and the molecular mechanism of congenital biliary tract malformations, experimental therapies such as organoid transplantation, cell therapy, and immunotherapy have been proved to be feasible. These advanced methods have shown outstanding advantages, particularly in patients with end-stage biliary tract malformations, surgery failure, and other problems that cannot be solved by conventional therapies. This review article discusses the potential pathogenesis of and promising therapeutic strategies for biliary tract malformations.