Objective To explore the clinical application effects of magnetic resonance imaging (MRI) and computed tomography (CT) in the diagnosis of pancreatic cystic lesions. Methods The clinical data of 68 cases of patients with pancreatic cystic lesions were retrospectively analyzed. The pathological biopsy results of fine needle aspiration were the gold standards for diagnosis, and the specificity, sensitivity, accuracy and imaging features of MRI and CT were compared in the differential diagnosis of pancreatic cystic lesions. Results The specificity of MRI was significantly higher than that of CT in the differential diagnosis of pancreatic cystic lesions (P<0.05), but there was no significant difference in sensitivity and accuracy between the two methods (P>0.05). The detection rates of polycystic and microcapsular changes, solid nodules and cyst fluid of pancreatic cystic lesions by MRI were significantly higher than those by CT (P<0.05). The detection rate of calcification by CT was significantly higher than that by MRI (P<0.05). Conclusion Both MRI and CT can make relatively accurate differential diagnosis of pancreatic cystic lesions, and MRI has more advantages because of its stronger specificity.