Purpose: We aimed to determine the association of iris color with lens thickness (LT) in a school-based sample of Chinese teenagers. Methods: In total, 2346 grade 7 students, from 10 middle schools, aged 13 to 14 years in Mojiang located in Southwestern China were included in the analysis. A grading system was developed to assess iris color based on standardized slit-lamp photographs. LT was measured by the LenStar LS900. Refractive error was measured after cycloplegia using an autorefractor and ocular biometric parameters, including axial length (AL), were measured using an IOL Master. Results: There was a significant trend of decreasing LTs with darker iris color. On average, eyes with "grade 1'' (the lightest) iris color, when compared with those with "grade 5'' (the darkest), had greater LTs (mean difference, 0.1 mm). After adjusting for other potential confounders including sex, height, and ALs in generalized estimating equation models, the trend was similar and did not change significantly. Compared with individuals with iris color of grade 1, those with grade 5 had a thinner lens of 0.1 mm (95% confidence interval [CI]: 0.01, 0.19) in sex-adjusted model and a 0.09 mm (95% CI: 0, 0.18) in multivariate-adjusted model. Conclusions: Lighter iris color might be associated with greater LTs in Chinese teenagers. The biological mechanisms underlying the association warrant further clarification.