Objective To investigate the value of MRI multi-sequence scanning combined with MRCP in the diagnosis of intrahepatic bile duct stones and bile duct obstruction. Methods To analyze the MRI and MRCP images of 50 patients with intrahepatic cholangiolithiasis with the obstruction of biliary identified by surgery from Jan 2013 to May 2016 in our hospital. Then classify and analyse of the imaging manifestations and other clinical manifestations of stones. Results The overall diagnostic rate of MRI multisequence scan combination with MRCP for intrahepatic cholangiolithiasis with the obstruction of biliary tract was 94%. The diagnosed rate of the different location: the left hepatic lobe diagnosed rate was 96.7%; the right lobe of liver in patients was 87.5%. The diagnosis rate of both left and right intrahepatic cholangiolithiasis was 91.7%. The diagnosis results were compared with the results of surgery confirmation, there is no statistically significant difference(P＜0.05). Conclusion MRI multi sequence scan combined with MRCP has a high accuracy rate in the diagnosis of intrahepatic bile duct stones and bile duct obstruction, which can guide role in the clinical treatment well.