The regulatory system of biological ryhthm consists of the central clock in the hypothalamic suprachiasmatic nucleus and peripheral clocks in peripheral tissues, responsible for coordinating the physiological functions of the body and maintaining normal life activities. The regulatory system of biological rhythm is involved in the regulation of cardiac function via neurohumoral and other pathways, whose disturbance is closely related to the occurrence of cardiovascular diseases. In recent years, a large number of studies have shown that the severity of myocardial ischemia-reperfusion injury has significant circadian variations. The adverse cardiac remodeling and heart dysfunction after ischemia-reperfusion injuries are related to clock genes, however, the precise mechanism has not been well clarified. Therefore, in this review,we summarize the role of clock genes in the occurrence of myocardial ischemia-reperfusion injury, providing a theoretical basis for the exploration of new strategies for the prevention and treatment of myocardial ischemia-reperfusion injury.