High altitude is closely related to intestinal mucosal damage and intestinal microbiota imbalance, and there is currently no effective prevention and treatment measures. In this study, the effects of stachyose (STA), L. rhamnosus GG (LGG) and their combination on inflammatory response, oxidatve stress and intestinal barrier function in mice exposed to acute hypobaric hypoxia were investigated. Our results indicated the combination of STA and LGG could more effectively regulate intestinal microbiota disorders caused by hypobaric hypoxia than STA or LGG alone. When mice were administered with STA + LGG, the content of short chain fatty acids (SCFAs) especially butyric acid significantly increased, which helped intestinal cells to form tight connections, improve the level of anti-inflammatory cytokine (TGF-β) and antioxidant enzymes (SOD, CAT, GSH-Px), and decrease the expression of pro-inlammatory cytokines and hypoxia-inducing factors (IFN-γ, IL-1β, IL-6, TNF-α and HIF-1α), thereby enhance the strong intestinal barrier function. Furthermore, the synbiotics significantly reduced the ratio of Firmicutes to Bacteroidetes, while significantly increased the relative abundance of Rikenella, Bacteroides, Odoribacter, Ruminiclostridium_5 and Gordonibacter, which were correlated with production of SCFAs and anti-inflammatory role. Correlation analysis showed that the protective effect of synbiotics on intestinal barrier function was associated with its anti-inflammatory activity and antioxidant capacity. It provided a strong foundation for further research on the role of STA and LGG in maintaining normal intestinal function at high altitude. Our study has identified and demonstrated a new synbiotic that may be one of the ideal intervention measures for preventing and treating intestinal dysfunction at high altitude.