The gut microbiota coexists symbiotically with the host, playing critical roles in physiological processes such as nutrient metabolism, immune regulation, and intestinal barrier function. However, the microgravity environment in space can significantly alter the composition and function of the gut microbiota, posing numerous challenges to astronaut health. A thorough understanding of the impact of microgravity on the gut microbiota during spaceflight, along with investigating the underlying patterns and mechanisms, is crucial for developing effective health protection strategies. This article synthesizes previous research to systematically elucidate the effects of microgravity on the gut microbiota, including changes in community structure, metabolic dysfunction, and associated pathways. It focuses on the regulatory effects of exercise intervention on the gut microbiota in microgravity environments. As a non-pharmaceutical approach, exercise intervention alleviates microgravity-induced microbiota dysbiosis and metabolic disorders through mechanisms such as regulating the gut-brain axis, influencing inflammatory signaling pathways, and improving intestinal motility and blood supply. This article aims to summarize the impact and mechanisms of microgravity on the gut microbiota, especially the role of exercise in improving intestinal microecological homeostasis, thereby providing theoretical support for astronaut health protection.