Objective: To investigate the prevalence and associated factors of congenital heart defects (CHD) among nursery, primary, and middle school students in Zhaotong, and to provide basis for CHD prevention strategies for children and adolescents. Methods: Using stratified random cluster sampling, a total of 11 343 nursery, primary and middle school students in 4 towns of Zhaotong were investigated with CHD screening and questionnaire during September to November in 2020. Results: The prevalence of CHD among nursery, primary and middle school students in Zhaotong was 11.99‰(95% CI =9.99‰-13.99‰), Yongshan County (14.90‰) > Yanjin County (10.22‰), rural (13.30‰) > urban (8.21‰)( χ 2=4.95, 4.77, P <0.05). Among 136 cases of CHD, the Ventricular Septal Defect (VSD) accounted the highest proportion (41.2%), followed by Atrial Septal Defect (ASD, 32.4% ), Patent Ductus Arteriosus (PDA, 14.0%), and Complex Congenital Heart Disease (CCHD, 5.9%) and the other CHD (others, 6.6%). The proportion of late diagnosed CHD was 50.74%, which was associated with living in rural areas of Yongshan County, low annual household income (10 000-<20 000 yuan), as well as isolated and uncomplicated CHD( OR =0.30, 0.13, 3.67 , 0.17, P <0.05). Conclusion Nursery, primary and middle schools students have the characteristics of high prevalence rate of CHD, large proportion of complex congenital heart disease, large number of late diagnosis and complex influencing factors in Zhaotong. It s in urgent need of strengthening learning prevention of CHD.