The biological clock can widely regulate the behavior and physiological function of human body.Studies have found that the intestinal tract itself also has biological clock rhythm and is regulated by the central biological clock rhythm. Circadian rhythm disorders widely relates to inflammatory bowel disease，irritable bowel syndrome，colorectal cancer and other intestinal diseases. Otherwise，biological clock rhythm disorders will also have an important impact on gastrointestinal motility，intestinal mucosal barrier permeability and intestinal flora，resulting in a variety of intestinal dysfunction or intestinal diseases. This paper mainly reviews the relationship of intestinal biological clock rhythm with the diseases and its mechanism.