Abstract: Objective To understand the effect of health education on the health literacy of middle school students in a main district of Chongqi,and to provide evidence for improving health literacy level in middle schools.Methods Cluster sampling method was used to select two middle schools respectively in rural and urban area,one school was taken as control group and the other was intervention group to have health education.The base-line survey was conducted in October,2016,and the final questionnaire survey was carried out in June,2017,the time for intervention lasted from March to May of 2017.Results After intervention,the rates of functional literacy and critical literacy of the students from the intervention school in urban area were 71.5% and 69.5%,respectively,higher than those of the control schools(62.2%,59.8%) (x2 =5.753,7.333,P<0.05).The level of overall health literacy and 3 sub-aspects in intervention group were lower than control group before invention in rural area,but the difference was of no statistical significance between control school and intervention school after the intervention(P>0.05).The level of functional literacy(urban:from 59.3% to 71.5%,rural:from 20.9% to 56.4%) and overall health literacy(urban:from 53.3% to 65.9%,rural:from 27.0% to 49.0%) among invention group between urban and rural city were higher than the level before invention (P<0.05).Conclusion The health education in school may improve the level of health literacy among middle school students.