Melatonin is produced to regulate the rhythmic behaviour of humans and other mammals. Biological rhythm represents a fundamental aspect of life and has been conferred by natural evolution. The activities that organisms perform during their lifetime are controlled and influenced by their biological rhythms. The pineal gland, located in mammals, serves as the regulatory centre for these rhythms and is responsible for synthesizing and secreting melatonin. Melatonin has an important role to play in the rhythmic behaviour of organisms. Previous analyses have mainly emphasised melatonin's pivotal role in circadian and reproductive annual rhythms, while neglecting its contribution to other annual rhythmic processes. This study aims to shed light on the regulation of melatonin in both circadian rhythm and annual rhythmic behaviour, focusing on the production and mechanisms involved. At the same time, it elucidates the intricate network of direct and feedback interactions that link melatonin to the biological clock and the neuroendocrine system. Additionally, it highlights melatonin's significant role in regulating biological rhythms, thereby serving as a point of reference for fundamental research on melatonin and future investigations into the endogenous biological clock mechanism in organisms. As mental disorders, such as circadian disorders, depression, and anxiety, become more common, studies have indicated a close correlation between melatonin secretion and these conditions. Consequently, it is imperative to explore the exact process by which melatonin governs biological rhythms, in order to furnish theoretical signposts for treating such disorders.