Organoid, formed from organ-specific cells, is a group of self-renewal and self-organizing cells growing in a 3-dimensional structure. With the recent progress on microenvironment regulation, stem cell differentiation and organ development, organoids have been constructed and used as promising tools for a wide range of multidisciplinary biomedical applications. Exercise disrupts the internal environment homeostasis, which brings a series of physiological alterations to the digestive system. The current animal or human models are necessary, but not sufficient to monitor the fluctuating microenvironment of gastrointestinal epithelial cells or hepatocytes during exercise. This review described the construction and application of digestive system organoids, as well as the effect of exercise on the microenvironment of intestinal epithelial cells and hepatocytes. The perspective applications of digestive system organoids in exercise physiology were also stated. Using organoid technologies, the possible mechanisms of the exercise-induced dynamic physiological changes would be explored in a new dimension.