With the development of social economy, the quality of national life has been rapidly improved, along with the accelerated aging of the population and the continued prevalence of metabolic risk factors. Cardiometabolic diseases (CMDs) have become a major disease burden for both urban and rural residents in China, and most of them are related to lifestyle changes in modern society, especially circadian rhythm disorders. Circadian rhythm regulating the activity of metabolism, such as carbohydrates, lipids, and other nutrients, is the most important pathway modulating the health. Nowadays, studies have shown that the interaction between circadian rhythmicity and gut microbiota counts for the homeostasis of metabolic health, while circadian rhythm disruption is associated with gut microbiota dysbiosis and metabolic diseases. However, there is a lack of research on the topic of gut microbiota mechanisms regulating circadian rhythm disruption leading to CMDs. With increased burden of CMDs prevention and treatment, as well as the demand of healthcare resource allocation, it prompts us to put forward a new strategy to solve this problem. This review focuses on the interactions between circadian rhythm and gut microbiota to elucidate the potential mechanisms of circadian rhythm disruption induced CMDs, providing a solid support for further prevention and treatment.