Background: Health education in primary and middle schools in China has been implemented for more than two decades since 1990s. This study aims to assess the students' health literacy gained through school health education, and provide scientific base to the concerned government agencies for updating the relevant national policy for school-based health education. Methods: The study was conducted through cross-sectional multi-stage cluster-stratified sampling survey in 77 elementary and 76 middle schools in 24 project provinces and two municipal cities in China. A self-administered questionnaire was developed. The reliability of the questionnaire was assessed using Cronbach's alpha and Spearman-Brown coefficient. A descriptive analysis was used to summarize the outcome. Results: The survey covered 8,008 subjects (4,011 from elementary and 3,997 from middle schools). The correct answer given on the majority of health knowledge was higher than 60% among the surveyed subjects. However, it was found that there were differences on student knowledge and practices from regions and economic levels; and the healthy personal behaviours between elementary and middle school students varied. Positive correlations between knowledge and practices, knowledge and attitudes were observed among subjects. Conclusions: Health literacy of the primary and middle school children in China was found to be limited and unbalanced. Thus school-based health education should be enhanced and the national guidelines for school health education and curriculum framework should be updated. (Contains 1 figure and 2 tables.)