Objective: To understand the public health emergency response capacity in primary and secondary schools, and to explore the problems and challenges in the prevention and control of public health emergency in primary and secondary schools for specific strategies. Methods: By using the stratified group sampling method, a questionnaire survey on general situation, knowledge, attitude and training, as well as public health emergencies response capacity among 2 988 teachers or leaders responsible for school emergency response in primary and secondary schools from Beijing, Chongqing and Yunnan. Results: Participants varied on their positions, titles, educational background and knowledge accuracy. Higher knowledge accuracy was associated with higher educational background ( χ 2=50.73-203.36, P < 0.05 ). The implementation of regular public health emergency related programs was poorly conducted in high schools (50.0%). Urban schools (42.0%) had higher proportion of qualified health care professionals than rural schools (18.2%), and private schools (48.5%) was higher than public schools (24.7%). The primary challenges included the shortage of guidance from professionals and the lack of related testing equipment (84.91%, 74.03%). Conclusion Although the ability of emergency handling of public health emergencies in schools in the three regions is advancing with the times, there are still many deficiencies, some omissions in the mastery of knowledge. It is suggested to inerease pre service and special training of school health work CDC should strengthen technical guidance and work supervision of infectious disease management in schools.