A complex mechanism of reduced number of bile duct innervating ganglion cells, smooth muscle distribution, foregut duplications, and abnormal pancreaticobiliary duct junction, which occurs during embryonic development and after birth in a genetic context, can lead to pathological congenital biliary dilatation. As a precancerous lesion of the biliary system, irrational treatment of congenital biliary dilatation will further increase the risk of malignancy in patients. By understanding the causes, pathological features, and limitations of early detection techniques of malignant tumor secondary to congenital biliary dilatation is helpful to clarify the key points in the management of congenital biliary dilatation, reduce the incidence of postoperative adverse treatment events and avoid the medical risk of secondary malignancy.