Neural tube defects (NTDs) constitute the most common type of birth defects. How much risk of NTDs could an area take? The answer to this question will help people understand the geographical distribution of NTDs and explore its environmental causes. Most existing methods usually take the spatial correlation of cases into account and rarely consider the effect of environmental factors. However, especially in rural areas, the NTDs cases have a little effect on each other across space, whereas the role of environmental factors is significant. To demonstrate these points, Heshun, a county with the highest rate of NTDs in China, was selected as the region of interest in the study. Bayesian belief network was used to quantify the probability of NTDs occurred at villages with no births. The study indicated that the proposed method was easy to apply and high accuracy was achieved at a 95% confidence level.