Objective To compare the application value of MRI and molybdenum target mammography in the differential diagnosis of benign and malignant breast lesions. Methods The clinical data of 78 patients with breast tumors confirmed by pathology treated in our hospital from May 2013 to May 2015 were analyzed retrospectively. Among them, 34 cases were with benign breast tumors and 44 cases with malignant ones. All patients received breast digital molybdenum target mammography and MRI examination after admission. The application value of MRI and molybdenum target mammography in the differential diagnosis of benign and malignant breast lesions was analyzed. Results Among the 78 cases of breast lesions, 30 cases of benign and 48 cases of malignant breast lesions were detected by molybdenum target mammography. The sensitivity, specificity and accuracy of it in the diagnosis of benign and malignant breast lesions were 80.0%, 79.2% and 79.5% respectively; MRI detected 34 cases of benign lesions and 44 cases of malignant lesions. The sensitivity, specificity and accuracy of MRI the diagnosis of benign and malignant breast lesions were 88.2%, 91.7% and 89.7% respectively. Conclusion The sensitivity, specificity and accuracy of MRI are higher than those of molybdenum target in the differential diagnosis of benign and malignant breast lesions. Breast molybdenum target mammography has its advantages in the diagnosis of small calcification but the MRI dynamic enhanced scan can clearly show the structure, character, edge, enhancement features of blood vessel and early enhancement features of breast soft tissues and improve the detection rate of benign and malignant lesions.