BACKGROUND Oddi sphincter plays an important role in preventing reflux cholangitis. There exists the controversy on application of choledochoduodenostomy in hepatolithiasis management. The present study aimed at evaluating long-term outcomes of choledochoduodenostomy for the treatment of hepatolithiasis. METHODS Forty-six consecutive cases of hepatolithiasis who underwent choledochoduodenostomy were analyzed retrospectively. The pre- and postoperative rates of recurrent cholangitis and acute cholangitis severe type were compared. Paired chi-square test was applied. RESULTS The mean follow-up time was 17.3 years ranging from 1.6 to 40 years with a follow-up rate of 97.8% (45/46). High rates of remnant stones (39.1%, 18/46), recurrent stones (31.1%, 14/45), uncorrected strictures (85%, 17/20), and mortality (24.4%, 11/45) were observed in this group. Regurgitation of food debris and duodenal content into the biliary tract through the anastomosis was observed. The rate of recurrent cholangitis was equal to the preoperative period (93.3%, 42/45). The rate of acute cholangitis severe type after choledochoduodenostomy (46.7%, 21/45) increased significantly (P<0.01) when compared to the preoperative period (20.0%, 9/45). CONCLUSIONS Choledochoduodenostomy did not entirely achieve the goal of clearance of stones, correction of strictures, and removing of hepatobiliary lesions by itself. Choledochoduodenostomy without cholangioplasty resulted in an increase of severe reflux cholangitis due to the loss of the anti-reflux function of the sphincter of Oddi. Therefore, choledochoduodenostomy is not an ideal approach to reduce cholangitis in hepatolithiasis and is not the best choice in the management of hepatolithiasis.