Objective To study 16-slice CT and 0.35T magnetic resonance cholangiopancreatography (MRCP) in the diagnosis of biliary system calculus. Methods 80 patients with biliary system calculi were selected as research subject, patients in the CT group (80 cases) were subject to 16-slice CT examination and patients in the MRCP group (80 cases) were subject to 0.35 T MRCP examination, surgical results serves as criterions to compare the advantages and disadvantages of two types of examinations. Results Surgeries confirmed that the positive rate of confirmation among patients in with calculus (93.75%) was higher than that of patients in the CT group (75.00%), and intergroup difference was significant (P<0.05). The diameter of calculus without bile duct dilatation of the MRCP group was less than 0.8cm, and the positive rate of MRCP group (93.33%) was higher than that of the CT group (68.89%), and the inter-group significant (P<0.05) was significant. Conclusion Clinically 0.35 T MRCP delivers higher positive diagnosis rate that that of 16-slice CT in the diagnosis of biliary calculi, and the diagnosis advantage of 0.35 MRCP was obvious especial for the calculus diagnosis with the diameter less than 0.8 cm without bile duct dilatation.