Traumatic brain injury (TBI) is characterized by high morbidity, high disability rate, and high mortality. In addition to treating intracranial injuries, treatment of TBI also requires attention to a series of secondary injuries and complications that occur after injury. The bidirectional signaling pathway between the intestinal microbiome and the central nervous system is known as the brain-gut axis. Research has confirmed that in the secondary injury of TBI, there exists a brain-gut axis with bidirectional regulation affecting the progression and prognosis of TBI, but the functional and mechanistic aspects of the brain-gut axis after TBI have not yet been fully clarified. This review will summarize and analyze the progress in research on the bidirectional regulation mechanism of the brain-gut axis after TBI.