Background: Self-harm and drinking were both serious problems in adolescents and many studies presented evidence of their association. However, gender difference in this association was seldom deeply discussed. Our study was aimed to evaluate the prevalence of self-harm and explore its association with drinking behaviors by gender and investigate the extent to which the gender differences exist in the association between self-harm and drinking.Methods: A total of 32362 students in grades 7 to 12 were anonymously surveyed using two-stage, stratified probability proportion sampling in Beijing, China. Self-harm, drinking behaviors and other basic information were obtained from anonymous questionnaire. Demographic variables and indicators of self-harm as well as drinking behaviors were analyzed with chi-square test and Gamma test between genders and the gender difference in this association was analyzed by log-binomial regression. Results: The total prevalence of self-harm was 13.7% with no significant gender difference (B=0.352, P=0.553). The prevalence of self-harm decreased with age in girls (G=-0.163, P<0.001). Self-harm was associated with drinking behaviors in both boys and girls. The Log-binomial regression demonstrated that girls in 15-19 years were at lower risk of self-harm than girls in 10-14 years while no age difference in boys. The higher OR for self-harm was found among girls with early drinking experiences compared with boys (1.863 vs 2.565). Girls who ever drunk (1.636 vs 2.211), were currently drinking (2.122 vs 3.400) and binge drinking (3.924 vs 6.357) had greater risk for self-harm than boys. Gender differences in self-harm were found at the following reasons of drinking, feeling down (4.402 vs 5.742), customary chronic drinking (3.945 vs 5.460), feeling delighted (1.806 vs 2.615), drinking with peers (1.797 vs 2.693). Conclusion: Self-harm has significant positive association with drinking among middle school students and girls with drinking behaviors were at higher risk of suffering self-harm. Identifying adolescents’ drinking behaviors is of vital importance to self-harm prevention and special attention should be focused on younger girls.