Objective To investigate the clinical value of magnetic resonance imaging (MRI) and color Doppler ultrasound (CDUS) in the localization diagnosis and qualitative diagnosis of biliary calculi. Methods The clinical data of 112 patients who were diagnosed with biliary calculi in our hospital from June 2107 to June 2018 were retrospectively analyzed. And patients were given MRI and CDUS within 2~14 d of the proposed biliary calculi treatment. Surgical or endoscopic retrograde cholangiopancreatography (ERCP) was used as the gold standard to compare the accuracy (sensitivity, specificity and accuracy rate) of MRI and CDUS in the diagnosis of biliary calculi. Results The sensitivity and accuracy rate of MRI in the diagnosis of biliary calculi were significantly higher than those of CDUS (P<0.05), and there was no significant difference in specificity (P>0.05). The diagnostic coincidence rate of MRI for biliary calculi was higher than that of CDUS. (P<0.05), and there was not statistically significant difference in the diagnostic coincidence rate of gallbladder, extrahepatic calculi and intrahepatic calculi (P>0.05). Conclusion Both MRI and CDUS can be used for the diagnosis of biliary calculi, but MRI qualitative and localization diagnosis has high accuracy.