Objective To investigate the awareness rate of malaria knowledge in primary and middle school students in Yangzhong City. Methods By stratified random sampling, we conducted a sample questionnaire survey in the primary and middle school students on their knowledge towards malaria. Results A total of 432 people were investigated, and 57.18% responded correctly to six or more questions in general. The awareness rate concerning malaria transmission , important symptoms, typical clinical manifestations, methods for diagnosis of malaria, the classification and hazards of malaria, treatment of malaria, options for medication, prevention strategies, eradication of the mosquitoes and World Malaria Day was 54.17%, 58.8%, 85.65%, 59.03%, 54.4%, 96.76%, 45.83%, 25%, 62.5% and 37.96%, respectively. Conclusion Primary and middle school students in Yangzhong city needs improving on their knowledge towards awareness of malaria, especially those from primary schools in rural areas.