Objective To evaluate the clinical effects of ultrasonography for structural examination in the diagnosis of fetal brain malformation and neural tube defects ( NTDs ) in early pregnancy . Methods A retrospective study was conducted to analyse 6 630 cases taking obstetric examination in Dongguan Maternal and Child Health Hospital from February 2014 to June 2015. The examination included a standardized ultrasound structural examination at 11-13 plus 6 weeks of pregnancy. The autopsied results of the induced fetus in early pregnancy from craniocerebral and neural tube structure malformation were investigated. All the cases were followed up concerning the outcomes and the malformation detection rate was calculated for analysis. Results The detection rates of exencephalus and anencephalus, holoprosencephaly, aphylly-holoprosencephaly, rachischisis, open spina bifida, and meningocele were 100%, 80%, 100%, 42.9%, 50% and 100%, respectively. The malformations which was missed in the early pregnancy but detected in the later gestational ages included:Dandy-Walker Syndrome, most of the non-open spina bifida, hypoplasia of the corpus callosum, foliaceous-holoprosencephaly and ventriculomegaly. Conclusions The structural examination using ultrasonography at early pregnancy is effective in the detection of severe open-neural tube defects. It′s worth generalizing in the cliical diagnosis but part of fetal malformations still need a further ultrasound examination in the mid-gestation or the later gestation.