The cornea functions as an optical lens and plays an important role in vision. For corneal diagnosis and treatment such as refractive surgery, a microscopic imaging system with a 3-D cellular resolution and retinal safety is strongly desired. Recently, confocal and multiphoton microscopies have been applied to corneal imaging with visible to near-infrared light sources. To increase retinal safety, an infrared light source is be needed. In this work, an infrared-based third and second harmonic generation microscopic study of mouse eyes is reported with ~700-μm penetrability and high cellular resolution. This study provides a critical reference for future development of infrared-based corneal imaging.