Objective To investigate the value of ultrasonography and magnetic resonance imaging (MRI) in prenatal diagnosis of fetal malformation. Methods A total of 466 fetuses with abnormalities or suspicious abnormalities diagnosed by prenatal ultrasonography selected and were examined by MRI. With the results of follow-up after birth as control, the diagnostic accordance rates of fetal malformation by ultrasonography and MRI were compared. Results In 466 cases of fetal abnormalities, the nervous system malformation was the most common (44.21%), followed by genitourinary system malformation (18.24%), chest deformity (13.95%), digestive system abnormalities (7.30%), fetal edema and tumor (6.22%), skeletal system and limb deformities (3.86%), heart malformations (3.22%), abdominal wall defects (2.36%) and facial anomalies (0.64%). Compared with results of autopsy and follow-up, the total accordance rate of MRI diagnosis of fetal malformation was 94.42% (440/466), which was significantly higher than that of ultrasound diagnosis [85.00% (396/466)] (P<0.05). Among 396 cases diagnosed with fetal abnormalities, 35 cases (8.84%) were found within 18 weeks of gestation, 153 cases (38.64%) were found in 18-24 weeks of gestation, 136 cases (34.34%) were found in 25-30 weeks of gestation and 72 cases (18.18) were found after 30 weeks of gestation. Conclusion Both of ultrasonography and MRI are of certain value in the diagnosis of fetal malformation. Using ultrasonography as the main screening method and rational use of MRI are helpful to improve the diagnostic accordance rate.