In mammals, the levels of gonadal hormones present circadian rhythm, which is controlled by the central circadian clocks and the suprachiasmatic nucleus. The disorder of circadian clock can change the internal environment of the body, while the circadian rhythm of gonadal hormones is destroyed, leading to the occurrence of some reproductive system diseases. In addition, gonadal hormones, such as estrogen and androgens, have effects on the central and peripheral circadian clock, play a role in the expression of clock genes, and affect the metabolism and reproduction. Therefore, to investigate the relationship between gonadal hormones and circadian clock system is crucial to understanding the development of reproductive system diseases. We explored the interaction between gonadal hormones and circadian clocks to further understand the occurrence and development of reproductive system diseases.