Objective To study the application value of ultrasound and magnetic resonance imaging (MRI) in the screening of suspected high-risk fetal central nervous system abnormalities. Methods Eighty-seven pregnant women with suspected highrisk fetal central nervous system abnormalities who were admitted in our hospital between October 2012 and October 2014 were enrolled in the study. Ultrasound and MRI examination were performed in all pregnant women. With the postnatal results or autopsy results of fetusesas the golden standard, the image quality and the detection rate of main abnormalities of central nervous system were compared between the two kinds of examination methods. The sensitivity, specificity, positive predictive value, negative predictive rate and accuracy were compared between ultrasound, MRI and the combination of the two. Results The image quality scores of ultrasound on blood flow display and choroid plexus ependyma display were significantly higher than those of MRI (P<0.05). The image quality scores of MRI on field of vision, resolution, tissue specificity, and display of the cerebral sulcus, fissure and gyrus were significantly higher than those of ultrasound (P<0.05). The coincidence rates of ultrasound in detection of Dandy-Walker syndrome and brain dysplasia (80%, 66.67%) were significantly lower than those of MRI(100%, 100%) (P<0.05). The coincidence rates of ultrasound in detection of microcephalus (100%) was significantly higher than that of MRI (0%) (P < 0.05). The accuracy rates of MRI and MRI combined with ultrasound (78.21%, 79.12%) were significantly higher than that of ultrasound (58.94%) (P<0.05). Conclusion The rate of ultrasound in the diagnosis of suspected high-risk fetal central nervous system abnormalities is high. MRI can supplement the results of ultrasound examination. The combined use of the two can improve the diagnostic accuracy rate.