Objective To evaluate effectiveness and safety of electronic choledochoscopy in treatment of intrahepatic bile duct stones. Methods From July 2013 to February 2016, 280 patients with intrahepatic bile duct stones in the Department of General Surgery of the Affiliated Hospital of Shandong Academy of Medical Sciences were selected as the research objects. All the patients were randomly divided into a choledochoscopy treatment group and a conventional treatment group by envelope principle method. There were 140 patients in each group. The safety and short- and long-term effectiveness were compared in these two groups. This study was approved by the ethics committee of the hospital. Results ① The age, gender, body mass index, course of disease, and location of stone had no significant differences in these two groups (P>0.05). ② The operations and the net stones were successfully completed in all the patients. The operative time was shorter, the blood loss was less, the incision length was smaller, the postoperative anal exhaust time was earlier, and the hospitalization time was shorter in the choledochoscopy treatment group as compared with the conventional treatment group (P<0.05). ③ The total postoperative complication rate on day 14 in the choledochoscopy treatment group was 2.9% (4/140), which was significantly lower than that in the conventional treatment group (11.4%, 16/140, P<0.05). ④ The curative excellent and good rates was 97.9% and 85.0% in the choledochoscopy treatment group and conventional treatment group respectively, which was a significant difference in these two groups (P<0.05). ⑤ The postoperative serum ALT and AST values on month 6 in the choledochoscopy treatment group were significantly lower than those in the conventional treatment group (P<0.05). Conclusion Electronic choledochoscopy in treatment of intrahepatic bile duct stones could promote rehabilitation of patient, reduce incidence of postoperative complications, and it is conducive to promoting recovery of liver function and improving follow-up effect.