Objective: To compare the clinical efficacy between anatomical segmentectomy/lobectomy and non-anatomical segmentectomy/lobectomy in treatment of intrahepatic bile duct stones. Methods: Ninety-six patients with intrahepatic bile duct stones were randomly divided into observation group and control group with 48 cases in each group. Patients in observation group underwent anatomical segmentectomy/lobectomy, while those in control group received non-anatomical segmentectomy/lobectomy. The operative time, intraoperative blood loss, incidence of postoperative complications and rates of residual and recurrent stones and reoperation of the two groups were compared. Results: Operations were performed successfully in all patients, and all of them experienced a smooth perioperative period. No death occurred. The operative times between the two groups showed no statistical difference (P>0.05), but the intraoperative blood loss, incidence of postoperative complications, rates of residual and recurrent stones and reoperation in observation group were all significantly lower than those in control group (all P<0.05). Conclusion: Partial liver resection is effective for intrahepatic bile duct stones and anatomical segmentectomy/lobectomy is the preferred procedure.