The purpose of the cross-sectional study is to describe the values and distribution of choroidal thickness and to explore its related factors, especially age, in Chinese children. A total of 3001 Chinese school children aged 6 to 19 years underwent comprehensive ophthalmic examinations, including axial length and cycloplegic refraction. Choroidal thickness was measured by swept-source optical coherence tomography (SS-OCT). There was a greater difference in the more central regions between the myopes and emmetropes. Multiple regression analysis was performed to determine the associated factors of choroidal thickness. The results demonstrated that age was independently positively related to choroidal thickness for emmetropes (β = 3.859, p < 0.001), and mild myopes with spherical equivalent greater than -2.00 D (-1.25 D < spherical equivalent ≤ -0.50 D: β = 3.476, p = 0.006; -2.00 D < spherical equivalent ≤ -1.25 D: β = 3.232, p = 0.020). However, no significant relationship between age and choroidal thickness was found in children with spherical equivalent ≤ -2.00 D, suggesting that the protective effect of physiologic choroidal growth with age against rapid axial elongation disappeared while axial elongation becomes the dominant determinant of choroidal thickness among children with myopia worse than -2.00 D.