There is no way to reverse spinal cord injury. In the case of spinal cord injury, patients always suffer from gastrointestinal dysfunction which impacts the quality of life. It has been reported that gut microbiota disorder after spinal cord injury is connected to the gastrointestinal dysfunction. Thus, this paper mainly explored the role of gut microbiota in vagus nerve system, hypothalamic-pituitary-adrenal axis and gut microbiota metabolites three pathways, and the relationship with gut inflammatory through gut microbiota changes after spinal cord injury.