Cholangiocarcinoma (CCA) is a common malignant biliary tract tumor in clinical practice. The detection rate of multi-slice spiral computed tomography (MSCT) with a diameter of 10 mm is low, and it is easy to be misdiagnosed and missed. In addition, patients who are allergic to iodized contrast media are not eligible for MSCT screening. However, magnetic resonance cholangiopancreatography (MRCP) is non-invasive, does not require contrast injection, scans quickly, and is simple to perform. MRCP has good development rate and the ability to recognize human pancreas and biliary tract. MRCP is also non-invasive, does not require contrast injection, has fast scanning speed, and is easy to operate. In addition, MRCP has a good development rate and the ability to recognize human pancreas and biliary tract. Therefore, this study sought to analyze the accuracy of MRCP and MSCT in the diagnosis of CCA. In this paper, 186 patients with highly suspected CCA admitted to the Second Affiliated Hospital of Soochow University from March 2020 to May 2022 were selected for MSCT and MRCP examination. We compared the diagnostic accuracy, sensitivity and specificity of MSCT and MRCP with pathological diagnosis and the detection rate of lesions with different diameters between MSCT and MRCP. Finally, the imaging features of MSCT and MRCP of CCA were analyzed. The results showed that (I) the diagnostic accuracy (95.70%), sensitivity (95.12%), and specificity (96.15%) of MRCP were higher than those of MSCT (69.89%, 60.98%, and 76.92%, respectively; P<0.05); (II) MSCT and MRCP were basically consistent with the datum (Kappa value =0.527, Kappa value =0.767, respectively); (III) the detection rate of lesions <0.5 cm in diameter of MRCP (32.05%) was higher than that of MSCT (14.00%; P<0.05); and (IV) the detection rates of lesions 0.5-1.0 cm (38.46%) and >1.0 cm (29.49%) in diameter of MRCP were lower those of MSCT (50.00%, and 36.00%, respectively; P>0.05). MRCP can provide relevant imaging feature information, improve the accuracy, sensitivity and specificity of the diagnosis of bile duct carcinoma, and has a high detection rate for small diameter lesions, which has good reference, promotion and reference value.