Abstract: Objective to compare and contrast the diagnosis results on 2D and 3D Ultrasonogrpahy against MRI. Method A 2D Ultrasonography was applied during a conventional prenatal sonography checking with a 3D Sonography assessment subsequently conducted to follow up on 49 fetus suspected of brain malformation.Furthermore, a MRI scan was taken within 24 hours after the 3D Sonography checking in our hospital as a final test. Data collections from all three assessments were completed, and an analysis of the comparisons of these three methods were done. Results Among these 49 fetus with confirmed or suspected brain malformation, there were two cases of misdiagnoses of Dandy-Walker Malformation assessed by 2D sonography, with a misdiagnosis rate of 40%, (P < 0.05) indicating a statistically significant result; misdiagnosis rate of Fetal Ventriculomegaly and Isolated Broadening Posterior Fossa were calculated as 26.7% and 33.3% respectively (P <0.05) , a statistically significant result. Overall, there were two cases with Cerebellum Malformation, from in which one case was identified by MRI, and the other one was misdiagnosed, with a misdiagnosis rate of 50.0%.In total, there were 2 cases of Holoprosencephaly, in which one was identified by Prenatal MRI, and the other was misdiagnosed (P < 0.05) , a statistically significant result. Conclusions All three assessments of 2D ultrasonography, 3D ultrasonography and MRI have their own advantages and disadvantages. In short, 2D Sonography is suggested to be applied for screening out cases with brain malformation, together with 3D Sonography as a complementary assessment. MRI can also be an effective and significant complement for sonography in completing and readdressing the final ultrasonic results.