Congenital biliary atresia (CBA) is an early neonatal biliary disease, which results in different degrees of intrahepatic and extrahepatic biliary atresia and liver fibrosis accompanied by irreversible injury of hepatobiliary duct. It is the main cause of neonatal obstructive jaundice and liver transplantation in children. Its pathogenesis has not yet been delineated clearly, and it is a complex disease caused by the combination of genetic and environmental factors. Hedgehog signaling pathway plays an important role in mammalian embryonic development, organ formation and development. Recent studies have found that Hedgehog signaling pathway also plays an important role in the of CBA. Activation of Hedgehog pathway can affect embryonic liver development, enhance the hepatobiliary fibrosis and hinder the formation of bile duct morphology, leading to the development of CBA. This article focuses on the important role of Hedgehog pathway in the formation of CBA.