Currently, the prevalence of gastrointestinal diseases remains high, common gastrointestinal diseases include irritable bowel syndrome, functional dyspepsia, and inflammatory bowel disease, etc., and these diseases seriously affect the physical and mental health of patients. The neural mechanism based on gut⁃brain axis provides new ideas for finding novel markers related to gastrointestinal diseases. In recent years, the research on the neural mechanism of gastrointestinal diseases based on MRI has attracted much attention. At the same time, some researchers have tried to use machine learning methods to analyze and interpret their image data, which has achieved favorable effects in deepening the understanding of the neural mechanism of gastrointestinal diseases. In this paper, the application status of machine learning methods in MRI neuroimaging related to gastrointestinal diseases is reviewed, aiming at providing references for deeply exploring neural mechanism of gastrointestinal diseases, and providing new ideas and novel approaches for improving diagnosis and prognostic evaluation efficiency of gastrointestinal diseases, etc.