Little is known about the role of association between ABO blood group and development of extrahepatic cholangiocarcinoma (ECC) through effects on hepatitis B viral (HBV) infection. Our aim was to address this question using a matched case–control study in Southern China.We prospectively analyzed 239 ECC patients, and 478 age- and sex-matched controls in Sun Yat-sen Memorial Hospital of Sun Yat-sen University from 1999 to 2011. Information on ABO blood group, HBV infection and other clinicopathologic factors was collected. Adjusted odds ratios (AORs) and the corresponding 95% confidence intervals (CIs) were computed from unconditional logistic regression models, adjusted for major confounding factors. The estimated AORs were as follows: A blood group, 1.784; HBsAg+/HbcAb+, 1.848 and HBsAg−/HbcAb+, 1.501. The A blood type had a significant effect on modifying the risk of ECC among subjects with HBsAg+/HbcAb+ (AOR 3.795, 95% CI 1.427–10.090). ECC patients with A blood group were more common in younger subjects, and a lower proportion of serum CA-125 and CA19-9 elevation in patients with blood type A was found. Our study suggests an association between A blood type, HBV infection and ECC risk, and a synergism between A blood type and HBV infection in the development of ECC.