The gut microbiota in Tibetan sheep's ruminant stomach varies across phenological phases, influencing nutrient absorption and adaptation. During the green grass period, acetic, propionic, and butyric acid concentrations in the rumen were higher than in the regreening and withered grass periods (P < 0.05). MCT1 expression peaked during regreening. Bacteroidetes dominated during the withered grass period (P < 0.01), with Rikenellaceae_RC9_gut_group and Prevotella most abundant in the rumen. Spatially, rumen VFA concentrations and MCT1 expression were significantly higher than in other stomachs (P < 0.05). Bacteroidetes, Prevotella and Rikenellaceae_RC9_gut_group were dominant across the ruminant stomach. Correlations between microbiota, VFAs, and transport genes highlight the interplay of fermentation, flora, and gene expression, crucial for Tibetan sheep's adaptation to the plateau environment.