The high-altitude, low-pressure, and hypoxia environment poses a significant threat to human health, particularly causing intestinal damage and disrupting gut microbiota. This study investigates the protective effects of Brassica rapa L. crude polysaccharides (BRP) on intestinal damage in mice exposed to hypobaric hypoxic conditions. Results showed that oxidative stress and inflammation levels were elevated in the hypoxia group, while BRP intervention significantly increased antioxidant enzyme activities (SOD, GSH-Px, T-AOC) and reduced inflammatory markers (IL-6, IL-1β, TNF-α). BRP also restored intestinal barrier function by enhancing claudin-1, occludin, and ZO-1 expression. Notably Chromatographic and metagenomic analyses revealed that BRP enriched butyrate levels, promoted beneficial bacteria like Akkermansia muciniphila and Leuconostoc lactis, and upregulated L-arginine biosynthesis II and L-methionine biosynthesis III pathways to enhance antioxidant activity. Fecal microbiota transfer experiments confirmed the role of gut microbiota in mediating BRP's protective effects, providing valuable insights into prebiotic-based therapeutic strategies for hypobaric hypoxia-induced intestinal damage.