Ermented dairy products have been used as excellent carriers of probiotics for more than one hundred years. In recent years, fermented dairy products have gain high popularity from consumers due to their high nutritional value, and health benefits including human metabolism-promoting property and human immune-improving function. It is well known that the gut microbiota plays very important roles in the body, including protection against potential pathogens, extraction of nutrients from dietary components, and regulation of digestion and immune homeostasis. Moreover, fermented milk can improve gastrointestinal function by regulating intestinal flora. This paper reviews the roles of fermented milk in improving gastrointestinal function by regulating intestinal flora, thereby alleviating diseases such as inflammatory bowel diseases, constipation, diarrhea, gastroesophageal reflux and peptic ulcers. The aim of this paper is to explore the main research progress on the roles of fermented milk in improving human gastrointestinal function, and provide reference for research and future development related to fermented dairy products.