Objective: To understand the influence of junior middle school students health literacy on knowledge, belief and behavior of COVID-19 in rural areas of Jiangxi Province, and to enhance junior middle school students ability to deal with public health emergencies. Methods: Stratified cluster random sampling was used to investigate the health literacy, knowledge level and behavior of COVID-19 protection of 4 311 grade 7 to grade 8 students in rural areas of Jiangxi Province; Chi square test and Logistic regression analysis were used to analyze the correlation between junior high school students health literacy and COVID-19 protection knowledge, belief and behavior. Results: The rate of health literacy of junior middle school students in rural areas was 18.21 %( n =785), the reported rate of intermediate level was high ( n =2 454, 56.92%), and the reported rate of junior high school students at a low level of health literacy was 24.87%( n =1 072). The rate of junior middle school students in rural areas with good COVID-19 protection knowledge was 63.49%, the rate of positive protection attitude was 74.25%, and the rate of good protection behavior was 85.36%; Rate of COVID-19 protection knowledge ( OR=4.85, 95%CI =3.80-6.18) and positive rate of protection attitude of high level health literacy ( OR=44.07, 95%CI =24.57-79.05), protective behavior possession rate ( OR=25.99, 95%CI = 19.67-34.35) were higher than those with low level of health literacy( P <0.01). Conclusion Health literacy is associated with COVID-19 protection knowledge, belief and behavior in rural junior high school students of Jiangxi Province, the findings provide direction for junior middle school students to improve their ability to deal with public health emergencies.