Objective: To explore the association of health literacy with overweight and obesity among middle school students in Chongqing, so as to provide evidence for obesity prevention and control strategies. Methods: From November to December 2019, a stratified cluster sampling method was used to select 7 851 middle school students from 8 complete middle schools across 4 districts/counties in Chongqing. Participants completed the Adolescent Health Literacy Questionnaire and underwent nutritional status assessments. Chisquare tests and multivariate Logistic regression analyses were performed to evaluate associations. Results: The prevalence of overweight and obesity among adolescents was 12.95%. The overall health literacy rate and rates for functional, interactive, and critical health literacy dimensions were 62.01%, 66.02%, 50.07%, and 72.42%, respectively. Significant differences in overweight and obesity prevalence were observed across districts/counties, urban/rural areas, sex, school stages, and onlychild status (χ2=25.93, 3.86, 80.55, 8.80, 6.43, P<0.05). After adjusting for confounding factors, multivariate Logistic regression revealed that middle school students with overall health literacy (OR=0.86, 95%CI=0.75-0.99), interactive health literacy (OR=0.85, 95%CI=0.74-0.97), and critical health literacy (OR=0.84, 95%CI=0.73-0.98) had a lower risk of overweight and obesity (P<0.05). Conclusions Health literacy is inversely associated with overweight and obesity among middle school students. Strengthening health education and improving interactive and critical health literacy may create favorable conditions for adolescent overweight and obesity prevention and control.