MicroRNA (miRNA), about 22 nt in length, are small single-strand RNA discovered in recent years that universally exist in the genome of creatures. They control physiological and pathological processes through regulation of gene expression at either posttranscriptional or translational level. Hundreds of miRNA have been confirmed to express in ocular tissues, and function as important regulators in physiological processes, including development, differentiation, regeneration after injury, as well as control of circadian rhythms in the eye. On the other hand, miRNA also play a crucial regulatory role in the pathogenesis and development of several ocular diseases, such as neovascularization, autoimmune uveitis, retinitis pigmentosa, glaucoma, and retinoblastoma. The mechanistic study on miRNA and their targets in physiology and pathology of the eye will provide the theoretical basis from which novel molecular therapy to ocular diseases stems.