To evaluate the clinical value of cholangioscopy guided selective cholangiography in treatment of complicated calculus of intrahepatic duct. Methods This study selected 96 patients with no calculus were found in patients with complicated calculus of intrahepatic duct by routine T-tube cholangiography and choledochoscopy after operation from August 2010 to July 2017. Under the guidance of choledochoscopy, selective cholangiography was performed to determine the location of calculus and bile duct strictures and take stone and relieve stenosis at the same time. Results 88 cases were found to have strictured bile duct combining with stones by selective cholangiography, 86 cases stones were removed by balloon dilatation of bile duct and Cook basket stone extraction. The average operating time is (58.4±11.5) min. 2 cases failed to get stones and then ended the operation. 8 cases of bile duct stricture without stone and directly received choledochoscopic high frequency electrotomy. There was no significant difference in distribution of intrahepatic stricture bile duct between the two groups (P>0.05). During lithotomy and electroresection, the bile duct tissue bleeding occurred in 8 cases but were resolved by endoscopic high-frequency electric cautery. After the operations, 9 cases of cholangitis and 4 cases of delayed hemobilia were observed symptomatic treatment. There was no significant difference in the incidence of complications between the two groups (P>0.05). The follow-up period ranged from 6 to 24 months. Hepatolithiasis recurred in 15 cases cured with PTBD and PTCS. Conclusions The standard selective cholangiography is an accurate and effective method for diagnosis and treatment of complicated calculus of intrahepatic duct or hepatolith combining with stricture of the bile duets.