Abstract: This review briefly introduces the principles of the atomic force microscopy (AFM) and its applications in ophthalmology. The AFM is an instrument that traces the surface topography of a sample with a sharp probe, while monitoring the interaction forces working between the probe and the sample surface. With AFM, the threedimensional image of the surface can be obtained in nearly physiological conditions at a nanoscale resolution, as well as the biomechanics of the sample. The domains of AFM application  have increased dramatically in recent years, from single molecules to organs. In ophthalmology, AFM demonstrates great advantages in the studies on eye microstructures and biomechanical properties, such as the cornea, sclera and lens. Although there are some innate limitations for AFM imaging and biomechanics measurement, AFM has great potential for providing valuable new informations in ophthalmology.