Objective To construct and apply a comprehensive information platform for the prevention and control of birth defects based on three-level prevention and control in the birth-age population of Yueyang City, aiming to improve the effectiveness of intervention and reduce the impact of birth defects on the fetus. Methods A retrospective analysis was used to study the married population of childbearing age in Yueyang from January 2017 to December 2019, all of whom were included in the comprehensive information platform for the prevention and control of birth defects based on the three-tier prevention and control. Observed indicators include birth defects I, II and III prevention and control and intervention effectiveness. Results (1) Effectiveness of prevention and control at the first level in each year: After continuous intervention, the education rate, marriage test rate and folic acid distribution in Yueyang city increased year by year, while the incidence of birth defects decreased year by year (P<0.05). (2) Effect of secondary prevention and control in each year: After continuous intervention, the serum screening rate, ultrasound diagnosis rate and amniotic fluid culture rate in Yueyang city increased year by year, while the birth defect rate decreased year by year (P<0.05). (3) Effectiveness of three levels of prevention and control in each year: After continuous intervention, the screening rate of newborns in Yueyang city increased year by year (P<0.05); and the disability rate of CH and PKU was 0% in three years. Conclusions The adoption of a three-level comprehensive prevention and control information platform in the prevention and control of birth defects has the advantages of safe, efficient and stable application, which is conducive to promoting the active conduct of prenatal examinations by pregnant women, enhancing the effectiveness of health education and improving the quality of health care during pregnancy, thereby effectively reducing the incidence, birth and disability rates of children with birth defects and achieving satisfactory graded application results. Accordingly, it is recommended that priority be given to the selection of a three-tier integrated information platform for prevention and control, depending on the actual situation.