Objective  To explore the effect of long-term soft contact lens wear on a unit area of corneal epithelium cell tissue， epithelial thickness， cell morphology and proliferating cell nuclear antigen （PCNA）； to inform about the effects of contact lenses on the cornea in clinical applications. Methods  This was an prospective case control study. Group A consisted of long-term （≥3 years） soft contact lens wearers （66 eyes of 33 patients） and control group B consisted of non-soft contact lens wearers （66 eyes of 33 patients）. The selected patients had undergone an excimer flap-free Epi-LASIK operation， and the corneal flap was removed with an Epi-K corneal epithelial knife. Ultrasound and microscopy were used for measurement of the corneal flap thickness and the basal cell count. Paraffin section and immunohistochemistry were used to study the morphological changes of the corneal flap， basal cells and the proliferating cell nuclear antigen. Data were analyzed using an independent t test. Results  After more than 3 years of soft contact lens wear， the thickness of the corneal epithelium was 55.33±4.56 μm and the number of basal epithelial cells were 3872.6±153.2 cells/mm2. The thickness of the corneal epithelium in the control group was 57.19±3.82 μm and the number of basal epithelial cells were 3989.2±289.6 cells/mm2. There was a statistically significant difference between the experimental and control groups （t=-2.422， -2.757， P＜0.05）. In the experimental group， corneal basal cells were arranged more loosely， the cells had less structured forms， and the basal membrane was thicker and rougher compared to the control group. PCNA positive cells could be found in corneal epithelial basal cells in the experimental group but not in the control group. Conclusion  Long-term wear of soft contact lenses can lead to corneal epithelium injury： the corneal epithelium thickness decrease， corneal epithelial basal cells decrease in number， the structure of the corneal epithelium developes a less organized pathology. There are also changes in cell morphology， cell-cell junctions， destruction of the basal membrane， and the presence of PCNA positive cells.