Objective To investigate the clinical value of preoperative magnetic resonance imaging (MRI) T2WI and magnetic resonance cholangiopancreatography (MRCP) in the diagnosis of common bile duct stones. Methods Patients with suspected common bile duct stones who admitted to the hospital from December 2015 to December 2017 were selected as subjects. All patients underwent MRI T2WI examination and MRCP within 2 weeks before endoscopic retrograde cholangiopancreatography (ERCP) and stone removal. With ERCP diagnosis and intraoperative findings as the golden standard, the accuracy rates, sensitivities, misdiagnosis rates and missed diagnosis rates of T2WI and MRCP in diagnosis of common bile duct stones were analyzed. Results The sensitivity, missed diagnosis rate and accuracy rate of MRI T2WI for diagnosis of common bile duct stones were 97.53%, 2.43%, 3.70% and 96.34%, respectively, while those of MRCP were 87.65%, 0.00%, 12.34% and 87.80%, respectively. The missed diagnosis rate of MRCP was significantly higher than that of T2WI (P<0.05). Conclusion The missed diagnosis rate of MRCP is high for ediment-like stones and solitary small stones, and the diagnostic efficiency for common bile duct stones is inferior to that of T2WI.