The circadian rhythm is a set of autonomous endogenous oscillators resulting nearly 24h cycles. The biological clock, including central and peripheral biological clock, is a clock system that regulates the circadian rhythm of the body. The biological clock gene and its encoded protein constituent the transcription-translation oscillation loop, which could regulate the circadian rhythm of biochemical, physiological, and behavioral processes through neural and humoral pathways. The mammalian eyeball contains a complete biological clock system, thus controlling the circadian rhythm of important physiological functions and various parameters of the eyeball. Abnormal circadian clock genes caused by various reasons will affect the circadian rhythm and may lead to the occurrence and development of the ocular diseases. Therefore, the pathogenesis and clinical manifestations of ocular diseases are characterized by diurnal variation. The change of circadian clock gene expression is not only involved in the pathophysiological process of ocular diseases, but also may be an important target for the prevention and treatment of diseases. This article introduces the circadian rhythm characteristics of corneal disease, glaucoma and myopia and the related biological clock regulation mechanism. Further research on the circadian clock provides a new strategy for the prevention and treatment of ocular diseases.