Objective To study the application of magnetic resonance imaging (MRI) and ultrasound in the diagnosis and differential diagnosis of fetal congenital pulmonary cystic adenomatoid lesions. Methods 110 patients with suspected fetal congenital pulmonary cystic adenomatoid lesions in our hospital between January 2013 and June 2016 were studied. All patients underwent MRI and ultrasound examination before delivery. After birth, 102 newborns received operation and pathological examination, and 8 cases were examined by autopsy. Results The sensitivity, specificity and accuracy of MRI were 98.98%, 83.33% and 97.27%, respectively while those of ultrasound were 97.94%, 41.67% and 91.74% respectively. The specificity and accuracy of MRI examination were significantly higher than those of ultrasound (P<0.05). Conclusion MRI has advantages of wide view and high resolution of soft tissue. Compared with ultrasound, MRI can be used for more accurate diagnosis and differential diagnosis of fetal congenital pulmonary cystic adenomatoid lesions, which is of important significance in comprehensive evaluation of the fetal status.