Objective To evaluate the intervention effect of peer-led education on the sexual health of rural left-behind middle school students and explore the health education mode suitable for rural left-behind students in West China. Methods Three rural schools in Dazhou, Sichuan province were sampled by the multi-stage cluster random sampling method. Six second grade classes of each school were selected and randomly divided into the peer-led education group, traditional education group, and control group. Data of questionnaire surveys before and after the intervention were analyzed to evaluate the short term effect (knowledge). Follow-up surveys of the peer-led education group and traditional education group were conducted after being intervened for six months to evaluate the medium and longterm effect (attitude and behavior). Results The awareness rate of sexual health knowledge of the peer-led education group increased from 49.4% to 75.3% and the average sore increased from 6.77±3.14 to 8.61±2.88 after being intervened. The differences were statistically significant (P=0.001). The awareness rate of sexual health knowledge of the traditional education group increased from 51.0% to 67.5% and the average sore increased from 6.89±2.91 to 7.41±3.11 after being intervened. The differences were statistically significant (P=0.024). The difference of the average sores of the control group before and after intervention was not statistically significant (P>0.05). The average sore of the peer-led education group immediately after intervention was 8.61±2.88, which was significantly higher than 7.41±3.11 of the traditional education group (P=0.000). The difference of the average sore was 1.19 (95%CI was 0.58-1.81). Follow-up surveys after six months showed that rates of positive attitude of the peer-led education group and traditional education group increased and rates of negative behavior decreased compared to those before intervention (P<0.05). The results of the peer-led education group were better than those of the traditional education group (P<0.05). Conclusion Sexual health education for rural left-behind middle school students is effective. The peer-led education method is more suitable. Changes of health attitude and behavior still need further study.