Objective A laser confocal microscope was used to investigate changes in the cornea from wearing orthokeratology lenses during the night. Methods In a retrospective case study， 60 people were chosen from patients at the Ophthalmology Department of the General Hospital of Nanjing Military Command during January 2009 to December 2012. Among them， 30 patients （total 60 eyes）， the experimental group， had worn orthokeratology night lenses for 2 years and the other 30 patients （total 60 eyes）， the control group， had never worn any form of orthokeratology. All patients underwent laser confocal microscopy examinations at the centre of the cornea， 2-3 hours after the experimental group had removed the orthokeratology lenses. An independent t test was used. Results Corneal surface shape may change significantly. Wrinkles could be observed from the epithelium to the anterior stroma. The subepithelial plexus was distorted and uneven in density but the stromal nerve and endothelial cell morphology were normal. The epithelial cell count was 4818±148， former stromal cells count was 1345±154， the rear stromal cell count was 799±76， and the endothelial cell count was 3025±193. All these counts were not statistically different from the control group. Conclusion Long-term orthokeratology lens wear during the night can induce changes in the corneal subepithelial plexus but there were no significant changes in stromal or endothelial cells.