Objective To investigate the clinical value of MRI diffusion-weighted imaging (MRI-DWI) and three-dimensional ultrasound in the differential diagnosis of benign and malignant breast masses. Methods 50 cases of patients with breast masses admitted to the hospital between May 2015 and February 2018 were examined by MRI-DWI and threedimensional ultrasound after admission. The former was used to analyze the morphological features and hemodynamics, etc. of breast masses and measure the apparent diffusion coefficient (ADC) values of normal breast tissues and visible lesions. The latter was used to analyze the three-dimensional ultrasound image score. Surgical excision or biopsy were performed to obtain results of pathological diagnosis. Results In the 50 patients, there were 31 cases (62.00%) of pathologically diagnosed benign masses and 19 cases (38.00%) of malignant masses. Analysis of variance showed that the mean ADC value of normal gland > benign masses > malignant masses (P<0.05). With ADC<1.26×10-3mm2 /s as the standard for malignant breast masses, the accuracy, sensitivity and specificity were 84.00%, 84.21% and 83.87%, respectively, and the area under the receiver operating characteristic (ROC) curve was 0.86. The rank sum test showed that there were statistically significant differences in three-dimensional contrast-enhanced ultrasound scores between benign and malignant breast masses (P<0.05). The accuracy, sensitivity and specificity of threedimensional contrast-enhanced ultrasound in the diagnosis of benign and malignant breast masses (76.00%, 68.42% and 80.65%) were lower than those of MRI-DWI. Conclusion Compared with three-dimensional contrast-enhanced ultrasound, MRI-DWI is more effective in the differential diagnosis of benign and malignant breast masses.