Background <p>This study aims to assess and compare the psychometric properties of EQ-5D-Y-3L and CHU9D in children and adolescents across different BMI classifications in Jiangsu, China. And to identify the more appropriate tool for BMI-related health related quality of life (HRQoL) assessment.</p> Methods <p>A multi-stage stratified random sampling approach was employed among children and adolescents aged 9 to 17 in Jiangsu Province. The feasibility, construct validity (including convergent, discriminant, and known-group validity) and ability to detect changes of these instruments were evaluated. Random forest models and restricted cubic spline analyses were utilized to examine factors associated with HRQoL.</p> Results <p>A survey of 37,574 participants (mean age: 13.53 years; 51.6% males) yielded complete data. The EQ-5D-Y-3L showed a higher ceiling effect (70.0%) than CHU9D (42.2%). Utility values for both instruments were highly correlated (<i>r</i> = 0.64), and the intraclass correlation coefficient (ICC) between the two utility values was 0.637. Moderate-to-high correlations were found in conceptually similar dimensions (<i>r</i> = 0.41–0.58, <i>p</i> &lt; 0.001). Significant differences were observed in the two utility values and EQ-VAS across different BMI classifications (<i>p</i> &lt; 0.001), with the CHU9D utility values and EQ-VAS demonstrating higher relative efficiency (RE &gt; 1) and effect sizes (0.038–0.218) compared to EQ-5D-Y-3L utility values (0.044–0.104). Age, gender, BMI, boarding at school, and parents’ education were significantly related to HRQoL (<i>p</i> &lt; 0.05).</p> Conclusions <p>Both EQ-5D-Y-3L and CHU9D show acceptable psychometric properties in Chinese children and adolescents, while utility values are not interchangeable. The CHU9D is recommended due to its superior ability to detecting changes and lower ceiling effect. Further study on the psychometric properties of EQ-VAS is needed.</p>