Confocal microscopy serving as an in vivo histological examination for cornea holds superiority in disease diagnosis, assessment and follow-up as well as physiological and pathological study due to it's real-time, non-invasive, quick operation with high-resolution imaging, and has been widely applied in ophthalmic clinic and research. This article reviewed the recent advances in the application of confocal microscopy in infectious or degenerative corneal diseases, and ocular surface diseases caused by systemic diseases.