Objective: To investigate the causes and treatment strategy of recurrent intrahepatic stones after choledochojejunostomy for biliary drainage. Methods: The clinical data of 28 patients with recurrent hepatolithiasis after biliary-enteric drainage treated during January 2006 to June 2013 were retrospectively analyzed. Results: According to whether or not the continuity of the extrahepatic bile duct was preserved in former surgery, the 28 patients were divided into preservation group and non-preservation group, respectively. Of the 16 patients in preservation group, in 8 cases with normal function of Oddi’s sphincter, the original biliary-enteric anastomosis was taken down, and after the bile duct was repaired, a T-tube was inserted for external drainage; 7 cases with Oddi’s sphincter dysfunction underwent resection and reconstruction of the biliary-enteric anastomosis, and then standard Roux-en-Y choledochojejunostomy was performed; and one case underwent choledocholithotomy only due to unresectable bile duct tumor. Of the 12 patients in non-preservation group, 7 cases with anastomotic stricture underwent anastomosic repair and reconstruction, and 5 cases underwent stone removal by incision of the anastomosis and then its reconstruction. Among the two groups, postoperative complications occurred in 11 patients (39.3%) which included biliary fistula in 3 cases, wound infection in 6 cases, and intra-abdominal bleeding in two cases, and were all resolved. No perioperative death occurred. The immediate stone clearance rate and final stone clearance rate in preservation group was 68.8% and 87.5%, in non-preservation group was 66.7% and 83.3% respectively, and the good rate of living condition during follow-up was 85.7% in preservation group and 90% in non-preservation group. All differences between the two groups showed no statistical significance (all P>0.05). Conclusion: For patients with recurrent intrahepatic stones after choledochojejunostomy, the former surgical procedure and cause of stone recurrence should be ascertained, stones should be removed as completely as possible, and method of biliary drainage should be chosen according to the function of Oddi’s sphincter.