Objective: To identify the latent class characteristics of health literacy and related factors among junior high school students, so as to provide evidence for developing precise and systematic health literacy promotion strategies. Methods: In November 2024, a two stage random cluster sampling method was used to conduct a questionnaire survey among 8 933 junior high school students in Zhongshan. Health literacy was assessed across six dimensions: health behavior and lifestyle, disease prevention and control, mental health, growth development and puberty health, safety emergency and risk avoidance, and medical knowledge and appropriate healthcare utilization. Latent profile analysis was used to identify distinct health literacy classes, and multinomial Logistic regression was applied to analyze the related factors. Results: Three latent classes of health literacy among junior high school students were identified: the well balanced type(71.7%，6 406), the medical knowledge deficit type(22.3%，1 992), and the overall low literacy type(6.0%，537). Logistic regression analysis showed that girls had lower risks of belonging to the medical knowledge deficit type( OR =0.53, 95% CI =0.48-0.59) and the overall low literacy type( OR =0.27,95% CI =0.22-0.33) compared with boys(both P <0.05). Students in rural schools had the highest risks of belonging to these two profiles above [ OR (95% CI ) =1.89 (1.61-2.21), 3.18 (2.50-4.06),both P <0.05]. Junior high school students having ≥2 siblings were positively associated with belonging to these two profiles, with risks 1.60 (95% CI = 1.35-1.89) and 2.25 times (95% CI =1.66-3.05) higher than those of only children (both P <0.05). Junior high school students with parental education of bachelor s degree or above were associated with lower risk of belonging to the medical knowledge deficit type (father: OR =0.63, 95% CI =0.47-0.84; mother: OR =0.68, 95% CI = 0.52 -0.90,both P <0.05). Junior high school students with receiving health education courses ≥3 times per month were associated with lower risks of belonging to both the medical knowledge deficit type and overall low literacy type ( OR =0.51, 95% CI =0.43- 0.60 ; OR =0.33, 95% CI =0.25-0.42, both P <0.05). Conclusions Three latent classes of health literacy exist among junior high school students in Zhongshan. Targeted interventions should be implemented based on profile characteristics, with an emphasis on strengthening medical knowledge education and providing comprehensive support for vulnerable groups.