Objective To understand the health literacy level of junior high school students in Hefei, and explore ways and means of improving their health literacy level, so as to provide basis for the development and evaluation of health literacy policy and intervention measures. Methods The stratified cluster random sampling method was used. Firstly, we select one junior high school randomly from each county in Hefei, and then we randomly select a class from grade two. All students in the class were included. Results The health literacy level of junior high school students was 3.5% in Hefei, and the proportions of the students with basic knowledge and ideas, healthy lifestyle and behavior, and basic skills were 32.1%, 26.8%, and 6.9%, respectively. The 6 kinds of health literacy level ranked from high to low were: the safety and first aid (52.9%), the scientific concept of health (47.8%), health information (24.8%), chronic disease control (21.2%), infectious disease prevention and control (19.0%), basic medical care (2.2%). There was statistically significant difference between urban and rural students in health literacy level (P< 0.01). There was no significant difference between male and female students in health literacy level (P> 0.05). Conclusion The health literacy level and basic skills of junior high school students should be enhanced. We should strengthen health education about basic medical, infectious disease prevention and chronic disease prevention, so as to improve the health awareness and self-care ability of medical treatment, and prevention of diseases.