Objective: To investigate the association between health literacy (HL) and health related quality of life (HRQoL) among primary and middle school students in Nanjing,and to provide a reference for improving health literacy and health related quality of life among children. Methods: In this cross sectional study, by using a multi stage rondom duster sampling method,a total of 4 388 primary (4-6), junior (grades 7-9) and senior (grades 10-12) high school students were randomly selected in Nanjing during May and June of 2018. HRQoL was measured as continuous variable with the validated Chinese version of Child Health Utility 9D (CHU9D CHN); the relationship between health literacy level and HRQoL was examined using mixed effect linear regression models and reported as mean difference ( MD ) and 95% confidence interval( CI ). Results: There were 85.8% participants who obtained adequate health literacy level, while the mean score of CHU9D CHN was (0.78±0.17) for overall participants. After control for potential confounding factors and class level clustering effects, participants who self reported adequate HL recorded an increased HRQoL scores of 0.08 (95% CI =0.06-0.10) units relative to those self reporting inadequate HL. According to the stratified analysis of students gender, school type and place of residence, the results show that after adjusting the relevant confounding factors and the aggregation of class level, compared with the students without health literacy, the score of health related quality of life of those with health literacy increased significantly. Conclusion Health literacy of primary school students in Nanjing is positively related to health related life qualities.Therefore,there is a need to promote student s health related quality of life through health literacy.