Objective To explore the application of MRI and three-dimensional ultrasound in the screening of prenatal fetal malformation. Methods A total of 90 cases of pregnant women who admitted to the hospital for production inspection from January 2016 to January 2018 were enrolled. All pregnant patients were given three-dimensional ultrasound and MRI. The detection efficiency of three-dimensional ultrasound and MRI were compared, and the detection rates of two detection methods for malformed fetuses in different parts were counted, and the detection rates of different types of malformed fetuses were counted. Results The accuracy rate, sensitivity and specificity in the diagnosis of fetal malformation were 86.67%, 89.16% and 57.14% by three-dimensional ultrasound, and were 92.22%, 93.98% and 71.43% by MRI. The follow-up results showed that there were 131 malformations, and the detection rates of MRI in craniofacial malformation and abdomen malformation were higher than those of three-dimensional ultrasound (P<0.05). The detection rates of MRI in the nervous system malformation and urinary system malformation were higher than those of three-dimensional ultrasound (P<0.05). Conclusion MRI has a high detection rate in prenatal fetal malformation screening.