Biological clock is a pattern of rhythms in which organisms exhibit cycles approaching 24 h in order to adapt to periodic changes in the external environment. Gut microbiota is the sum of extremely large number of microorganisms parasitized in humans and animals. Disorders of the biological clock increase the risk of metabolic diseases, and the occurrence of these disorders is closely related to the interaction with the dysbiosis of the gut microbiota. With the deepening of the understanding of the brain-gut axis, targeting gut microbiota to ameliorate biological clock disorders and associated diseases has achieved major theoretical breakthroughs and was partially applied in clinical practice, including dietary interventions such as time restricted feeding, development of microbial-related products (probiotics and postbiotics), and fecal microbiota transplantation. This article reviews the research progress of intestinal flora and rhythmicity, as well as targeting intestinal flora for the treatment of biological clock disorders, so as to provide new ideas for the prevention and treatment of rhythm disorders and concurrent diseases.