The relationship between exercise and cardiac health has always been a hotspot in the fields of medicine and exercise science. Recently, with the in-depth study of the biological clock, people have gradually realized the close relationship between cardiac metabolic activity and circadian rhythms. The mammalian circadian system includes the central circadian clock and peripheral circadian clocks, the central circadian clock is the main clock system responsible for regulating the circadian rhythms in organisms, located in the suprachiasmatic nucleus (SCN) of the hypothalamus in mammals, which receives light signals from the retina and translates them into neural signals to regulate peripheral circadian clocks distributed throughout the body. Peripheral circadian clocks exist in various tissues and organs of organisms, coordinating with the central circadian clock to maintain the circadian rhythms of the organism. A series of clock genes regulate downstream clock-controlled genes through the transcriptional-translational feedback loop (TTFL), profoundly affecting the physiological activities of the heart, including cardiac contraction, relaxation, and metabolic processes. Factors such as sleep disorders, shift work, light pollution, and excessive use of electronic devices in modern lifestyles have led to widespread disruption of circadian rhythms, which are significantly correlated with increased cardiovascular disease incidence and mortality. Studies have found that dysregulation of the cardiac circadian clock can not only lead to myocardial lipid degeneration and weakened metabolic rhythms but also decrease myocardial glucose utilization, thereby increasing the risk of adverse cardiac events. Exercise, as a key zeitgeber, has been widely demonstrated to regulate the circadian clocks of peripheral organs such as skeletal muscle, kidneys, and liver. Additionally, exercise, as an important means to improve cardiovascular function, can effectively enhance cardiac metabolic function and resistance to stress stimuli, playing a significant role in promoting heart health. However, the specific mechanisms by which exercise affects the cardiac circadian clock and its related genes are currently unclear. Therefore, this review will focus on the relationship between the cardiac circadian clock and cardiac metabolic activity, summarize previous research to review the possible mechanisms of exercise-mediated regulation of cardiac metabolic activity on the cardiac circadian clock. The cardiac circadian clock plays an important role in maintaining cardiac metabolic activity and physiological functions. The loss of cardiac circadian clock genes Bmal1 and Clock can significantly reduce cardiac fatty acid and glucose utilization rates, increase myocardial lipotoxicity, weaken the circadian rhythm of myocardial triglyceride metabolism, and lead to abnormalities in the circadian clocks of other peripheral organs. Exercise, as a zeitgeber, can independently regulate the cardiac circadian clock apart from the central circadian clock. Additionally, exercise, as an important means to improve cardiovascular function, may regulate cardiac metabolic activity and the transcription of clock genes by activating the hypothalamic-pituitary-adrenal axis (HPA) and sympathetic-adrenal-medullary axis (SAM) and regulating energy metabolism, thereby maintaining the stability of the cardiac circadian clock and promoting heart health. Future research on the molecular mechanisms of exercise regulation of the cardiac circadian clock will help clarify the role and impact of clock genes in cardiac metabolism and physiological activities, providing new preventive and treatment strategies for shift workers, night owls, and patients with cardiovascular diseases. Therefore, future research should focus on (1) the mechanisms by which exercise regulates cardiac metabolic activity and the circadian clock, (2) the effects and mechanisms of exercise on the disruption of cardiac circadian clock induced by light-dark cycle disturbances, and (3) the effects of exercise on the metabolic activity and circadian rhythms of other peripheral organs regulated by the cardiac circadian clock.