Objective To summarize the sonography characteristics and improve endoscopic diagnostic ability for cholangiocarcinoma by comparing the manifestation of intraductal ultrasonography between cholangiocarcinoma and benign bile duct stricture. Methods This was a single center retrospective case control study. A total of 52 patients who took ERCP and IDUS examination with definite diagnosis of cholangiocarcinoma during January 2012 and January 2017 were included in this study, and 59 patients who took the examination during the same period with definite diagnosis of benign bile duct stricture were included as control. Clinical data, laboratory examination, manifestation of IDUS (length of stricture, hypoechoic or not, thickness of bile duct, symmetry, existence of outer membrance destruction) were collected and compared between two groups. Results Clinical manifestation and results of laboratory examination didn’t show significant difference between cholangiocarcinoma and benign bile duct stricture. Intraductal brushing cytology and forceps biopsy showed 28.9% and 40.0% malignant evidence respectively. IDUS showed thicker bile duct in cholangiocarcinoma group (6.8±4.0 VS 4.1±2.3mm,p<0.01). Proportion of hypoechoic and nonsymmetrical thickened bile duct were higher in cholangiocarcinoma group (78.8% VS 44.1%,92.3% VS 50.8%,respectively, p<0.01). 8 cases (15.4%) in cholangiocarcinoma group showed outer membrance of bile duct destruction whereas none was seen in control group. Conclusion Hypoechoic nonsymmetrical thickened on intraductal ultrasonography may indicate the diagnosis of cholangiocarcinoma, while destruction of bile duct outer membrance completeness is highly suspicious for the diagnosis of cholangiocarcinoma.