Objective: To investigate the long-term effect of orthokeratology on the choroidal thickness and choroidal contour in myopic children. Methods:Subjects were from a conducted 2-year Randomized Clinical Trial. Children (n=80) aged 8-12 years with spherical equivalent refraction of -1.00 to -6.00 D were randomly assigned to the control group (n=40) and ortho-k group (n=40). OCT images were collected at the baseline, 1-, 6-, 12-, 18-, and 24-month visits, then the choroidal thickness and choroid contour were calculated. Axial length (AL) and other ocular biometrics were also measured. Results: During two years, in the control group, the choroidal thickness became thinning and the choroidal contour became prolate with time at all visits (all P<0.001). Ortho-k can improve the choroidal thickness (all P<0.001) and maintain the choroidal contour at all visits (all P<0.05). In the ortho-k group, the choroidal contour was less changed in the temporal than nasal (P=0.008), and the choroidal thickness was more thickening in the temporal 3 mm (P<0.001). Two-year change in choroidal thickness was significantly associated with the two-year AL change in the control group (r=-0.52, P<0.001), however, this trend was broken by ortho-k (r=-0.05, P=0.342). After being adjusted by other variables in the multivariable regression model, the effect of ortho-k on choroidal thickness was stable. Conclusions: In a short term, ortho-k can improve the choroidal thickness and maintain the choroidal contour, but this effect diminished in a long term. Further study with larger sample size and longer follow-up is warranted to refine this issue.