To evaluate the time trends in the prevalence of neural tube defects and all their subtypes as well as to identify the epidemiological characteristics of these malformations documented in the Liaoning Province of northeast China from 2006 to 2015. This was a population-based observational study using data from 3,248,954 live births as well as from 6217 cases of neural tube defects, 1,600 cases of anencephaly, 2,029 cases of spina bifida, 404 cases of encephalocele, and 3,008 cases of congenital hydrocephalus from 14 cities in Liaoning Province from 2006 to 2015. All analyses were conducted using SPSS software. During the observational period, the prevalence of neural tube defects, anencephaly, spina bifida, encephalocele, and congenital hydrocephalus was 19.1, 4.9, 6.2, 1.2, and 9.3 per 10,000 live births, respectively. Significantly decreasing trends were observed in the prevalence of all these malformations except for encephalocele. Notably, relatively higher prevalence rates were found in isolated compared with non-isolated malformations, with significant differences in selected characteristics (e.g., prognosis status, gestational age, and birth weight) between isolated and non-isolated cases of these malformations. The prevalence of neural tube defects showed a downward trend in Liaoning Province from 2006 to 2015. However, more attention should be focused on non-isolated cases in the future because of the severe clinical manifestations. Future prevention efforts should be strengthened to reduce the risk of these malformations, especially the non-isolated subtype, in areas with high prevalence.