Objective To study the role of ultrasound and MRI in the screening of fetal heart malformation and provide theoretical basis for finding more reasonable and effective inspection methods. Methods 7438 cases of pregnant women in prenatal examination in our hospital from December 2014 to December 2017 were selected and divided into two groups of second trimester (20~28 weeks, n=5132) and third trimester (28~36 weeks, n=2306) according to gestational age, and the two groups were examined by ultrasonic rapid scanning, echocardiogram and MRI respectively. The results of three inspection methods for fetuses were compared and analyzed. Results There were 64 cases (0.86%) with heart malformation in induced labor or after birthamong 7438 cases of fetuses, and 54 cases (84.38%), 57 cases (89.06%) and 58 cases (90.63%) were detected by routine B ultrasound scan, 2D FIESTA and echocardiogram respectively. The detection rates of three inspection methods were 88.37%, 86.05% and 93.02% respectively in the second trimester, and were 76.19%, 90.48% and 85.71% respectively in the third trimester. Conclusion B ultrasound and MRI have advantages and disadvantages in prenatal screening for fetal heart malformation. Under normal circumstances, fetal ultrasonic rapid scanning can basically complete the screening with low rate of missed diagnosis, and supplement echocardiogram for diagnosis of suspicious cases. MRI is of late development but rapid progress, and 2D FIESTA sequence can make up for the lack of ultrasound in many ways from the perspective of prenatal diagnosis of fetal heart malformation, therfore it can be used as an effective supplementary means.