Absence of the bifurcation of the portal vein is an extremely rare anomaly and the misled ligation of the portal vein would result in the lethal hepatic failure. In this paper, a resected case of hilar cholangiocarcinoma with this anomalous portal venous system is first presented. Preoperative percutaneous transhepatic portography disclosed an absence of portal bifurcation and a transversely running portal vessel from the right anterior segment to the left lateral segment. The patient underwent left hepatic lobectomy with caudate lobectomy, in which the portal trunk was successfully preserved.