Objective This paper is to investigate the multi-center comparative analysis on diagnosis value of conventional ultrasound and MRI for fetal abnormalities. Methods Fifty pregnant women with fetal abnormalities admitted by the outpatient of obstetrics confirmed by conventional ultrasound diagnosis undergoing MRI examination, to follow-up results and clinical pathologic results after birth were treated as standards to conduct multi-center comparative analysis, and diagnostic value of MRI and conventional ultrasound clinical was objectively evaluated. Results The fetal abnormalities from 50 pregnant women are mainly focused chest deformity, accounting for 26.0% approximately, followed by central nervous system abnormalities at 22.0%. The diagnosis accuracy and specificity after statistics χ2 test satisfied(P＜0.05) , the differences was significant, and there was not obvious difference in the sensitivity (P>0.05). Conclusion (1) MRI delivers high accuracy and specificity in the diagnosis of fetal abnormalities.(2) conventional ultrasound was susceptible to be interfered in the diagnosis, but it is featured with simple operation, low cost and relatively high clinical diagnosis rate, thus can be used as a major means for screening.(3) the authors suggest joint diagnosis of two ways should be applied in clinical diagnosis of fetal abnormalities in order to improve the diagnosis rate, and can the waste of medical resources may be avoided.