Objective To investigate the diagnostic efficacy of color Doppler ultrasound and magnetic resonance imaging (MRI) examination on malformation of fetal central nervous system. Methods 100 pregnant women suspected whose fetus had malformation of central nervous system treated in our hospital from January 2014 to January 2018 were enrolled. The postpartum fetal examination or result of autopsy were used as the gold standard to compare the detection rate, sensitivity and specificity of different examination for the diagnosis of malformation of central nervous system. And the imaging features of deformed fetuses in different examination were compared. Results The coincidence rate of ultrasonography in the diagnosis of microcephaly was significantly higher, and the coincidence rate of MRI in diagnosis of dysplasia of brain and occlusion syndrome of the fourth ventricle was significantly higher (P<0.05). The sensitivity of MRI alone and MRI combined ultrasonography in the diagnosis of malformation of fetal central nervous system was significantly higher than that of ultrasonography (P<0.05). The image quality of MRI was significantly higher than that of ultrasound (P<0.05). In color Doppler ultrasonography, the skull of the fetus with encephalocele showed high echo with continuous interruption.In the microcephaly fetus, the fetal head circumference is significantly reduced.In fetus with cyst of choroid plexus,the choroid plexus showed a circular anechoic area,coronal section and sagittal section in agenesis of the corpus callosum in the ultrasound examination failed to show,ultrasound examination did not clearly show brain dysplasia, and the head circumference partly was significantly reduced. In the MRI examination, the fetus can be characterized by enlarged occipital angle of the ventricle, abnormal changes in the lateral ventricle in the form of "drops of water", corpus callosum was not observed in the sagittal and coronal positions, and the cerebellum and thalamencephalon were clearly displayed,but MRI can not detect microcephaly. Conclusion Color Doppler ultrasound and MRI have similar diagnostic rates for malformation of fetal central nervous system. However, the image quality of MRI is higher, and the sensitivity of combination of two examinations is higher. Therefore, the two examinations can be combined to complement each other, which is more beneficial for the diagnosis of malformation of fetal central nervous system.