To perform safe and successful corneal refractive surgery on myopic patients, corneal thickness (CT) and corneal epithelial thickness (CET) must be accurately measured. Numerous individuals with myopia wear soft contact lenses (SCLs) for the correction of visual acuity but may subsequently undergo corneal refractive surgery. The aim of the present study was therefore to investigate the effects of long-term SCL wear on the CT and the CET of myopic subjects in order to guarantee the safety and accuracy of subsequent corneal refractive surgeries. Fifty-six subjects prepared to receive refractive surgery at Jinan Mingshui Eye Hospital (Zhangqiu, China) from April to July 2013 were included in the study. CT and CET were measured in subjects immediately following discontinued SCL wear (group I, 56 eyes), and subsequently following >two weeks of discontinued SCL wear (group II, 56 eyes). Ninety-four subjects with no history of corneal contact lens wear were enrolled as a control group. The CT and CET were measured at positions with a radius of 0.0‑1.0, 1.0-2.5 (divided into eight quadrants) and 2.5-3.0 mm (divided into eight quadrants) away from the corneal center using the RTVue-100 Fourier-domain anterior segment optical coherence tomography system. A significant decrease in the CT of the subjects in group II was observed, compared with that of group I and the control group (P<0.05). A significant decrease was observed in the CET of groups I and II compared with that of the control group (P<0.05). Following discontinuation of SCL wear, CET increased. However, the increased CET was unable to reach the normal range exhibited by the control group. Edema and thinning of the corneal stroma, as well as thinning of the corneal epithelium were observed in groups I and II. In conclusion, it was proposed that in clinical practice, for myopic patients following long-term SCL wear, CT and CET should be determined ≥ two weeks following discontinuation of SCL wear, once a stable CT and CET are obtained.