•This article compared the clinicopathological differences between the cystic duct carcinoma and type I/II perihilar cholangiocarcinoma. •This article compared the efficacy of routine imaging examinations to distinguish between the cystic duct carcinoma and type I/II perihilar cholangiocarcinoma. •This article suggested NLR and GS as new indicators for the differential diagnosis of the cystic duct carcinoma and type I/II perihilar cholangiocarcinoma.