AIM: To examine the profile of the choroidal thickness (CT) in healthy myopia subjects and emmetropic participants by Heidelberg Eye explore software and Image J software so as to compare the agreement and reproducibility of the two methods. METHODS: Thirty-six study participants (36 eyes) were enrolled in this research. The fovea and parafoveal region (the region of 6mm diameter of the fovea as center) of the images were selected by spectral domain optic coherence tomography (SD-OCT). The choroidal thickness was measured manually by the Heidelberg Eye explore software (version 5.3.3.0, Heidelberg Engineering) with a vertical line and the Image J software with a line vertical to the retinal pigment epithelial layer. The agreement and reproducibility of the two methods were described by the Bland-Altmann analysis. RESULTS: As compared with Heidelberg Eye explore software (39.9186), the repeatability coefficient is lower calculated by Image J software (27.3525). The Bland-Altmann analysis showed that the limits of 95% CI of agreement analysis is -18.437-63.949μm and the upper limits of the precision of the 95% CI of agreement is between 16.102 and 111.796μm and the lower limits is range from -66.29-21.41μm, which reflected a great variations of the difference. CONCLUSION: The repeatability and agreement of measurement implied by Image J software was better than the Heidelberg Eye explore software. The Image J software should be used for measuring the choroidal thickness in future study in China.