Objective To identify factors related to the knowledge, attitude and practice KAP of birth defects prevention among pregnant women, and provide reasonable suggestions to improve perinatal health services and health education. Methods Using cluster sampling method, 5500 participants from pregnant women school were enrolled. Information on “awareness of basic knowledge of birth defects” and 7 questions about attitudes and practice to participant actual situation was gathered through personal interviews using a structured questionnaire. The related factors were analyzed by classification tree model of SPSS 19.0. Results As to birth defects related knowledge, prospective return was more than 50% in the pregnant women with junior, senior high school and technical secondary school education level. As to birth defects prevention faith, the main determinant was census register types; prospective return of pregnant women who were local permanent residents and floating population aged ≥25 years was 95.9%. The main influencing factor of practice was prenatal doctor's education; prospected return was 62.3% after strengthening the health education of prenatal doctor. Conclusion In order to improve birth defects education effect, pregnant women who have junior, senior high school and technical secondary school education level and are local permanent residents or floating population aged ≥25 years should be key targeted population. Prenatal doctor's health education will be a powerful guarantee.