PURPOSE. To explore the associations between macular choroidal and retinal thickness and axial elongation in non-myopic and myopic junior students. METHODS. In this school-based longitudinal observational study, axial length was measured by optical low-coherence reflectometry, and choroidal thickness and retinal thickness were measured by spectral-domain optical coherence tomography. Myopia was defined as non-cycloplegic objective spherical equivalent refraction <= -0.50 diopters. Structural equation modeling and multiple linear regression models were used to analyze the associations between baseline choroidal and retinal thickness with axial elongation. RESULTS. Out of 1307 students examined at baseline in 2017, 1197 (91.58%) returned for follow-up examination in 2018, with a median age of 12.00 years (interquartile range [IQR], 1.00) and included 667 boys (55.72%). Within a 1-year period, the median axial elongation of right eyes was 230 mu m (IQR, 180) in boys and 200 mu m (IQR, 160) in girls (P = 0.032). The thinner temporal choroidal thickness was associated with greater 1-year axial elongation only in myopic students (beta, -0.20; 95% confidence interval [CI], -0.37, -0.03), the thinner temporal retinal thickness was associated with greater 1-year axial elongation in both non-myopic (beta, -2.67; 95% CI, -4.52, -0.82) and myopic (beta, -0.99 ; 95% CI, -1.68, -0.30) students, after adjustment for sex, age, and height. Subfoveal and nasal choroidal and retinal thickness were not significantly associated with axial elongation in either non-myopic or myopic students. CONCLUSIONS. A thinner temporal choroid at age 12 years may predict greater 1-year axial elongation in myopic students, and a thinner temporal retina may predict greater 1-year axial elongation in both non-myopic and myopic students. This finding may help to identify children at risk and control axial elongation with potential preventive strategies.