Malignant obstructive jaundice is caused by tumors arising from the head of the pancreas and biliary tree, or seen due to secondary metastases in the porta hepatis lymph nodes. Magnetic resonance cholangiopancreatography (MRCP) is a non-invasive diagnostic technique that can be used for imaging the entire biliary tree and pancreatic duct system. The objective of this study was to evaluate the accuracy of MRCP in the diagnosis of malignant obstructive jaundice. The methods used involved comparative review of the images obtained by using magnetic resonance imaging and MRCP as well as comparison between MRCP- and pathology-based diagnoses. The accuracy of MRCP-based diagnosis of malignant obstructive jaundice was analyzed. Our data show that the positive rate of anatomical diagnosis and the detection rate of bile ducts on the proximal side of obstruction are 100%. The diagnostic accuracy of malignant obstruction was 82.9%. MRCP was found to have high diagnostic specificity for determining the location and extent of obstruction. We, therefore, concluded that MRCP had significance for clinical diagnosis of malignant obstructive jaundice. The positive rate of localization diagnosis was 100%. Distinguishing the quality of obstruction was also important. The diagnostic accuracy of MRCP for malignant obstructive jaundice was remarkably higher.