Tibetan pigs exhibit remarkable adaptability to hypoxic high-altitude conditions. However, metatranscriptomics has not been used to investigate the transcriptional activity and functional responses of the gastrointestinal microbiota as part of their adaptation to high altitude. We collected 57 samples of the contents of the stomach, jejunum, cecum, colon, and rectum of six high-altitude Tibetan pigs (n = 6, elevation 3750 m) and six low-altitude black pigs (n = 6, elevation 500 m) for metatranscriptomic analysis. We identified 79 differentially abundant bacterial genera and 69 differentially abundant bacterial species. In particular, Lactobacillus crispatus and Lactobacillus delbrueckii were significantly more abundant in the gastrointestinal microbiota of the high-altitude Tibetan pigs than in that of the low-altitude black pigs. Functional analysis revealed differences in transcripts associated with energy, carbohydrate, and amino acid metabolism. The microbial correlation network of Tibetan pigs contained more nodes and edges than that of black pigs. Consistent with this, within the CAZyme database, the CBM32 family of carbohydrate-binding modules and GH27 glycosidases were significantly enriched in the Tibetan pig samples, suggesting that these enzymes may play a crucial role in energy acquisition and carbon source metabolism in these pigs. These findings provide insights into the gastrointestinal microbial characteristics of Tibetan pigs and black pigs. In summary, these changes may enhance the stability of the gut ecosystem of Tibetan pigs and improve their energy utilization in nutrient-deficient high-altitude environments. These findings suggest that the gut microbiota may contribute to metabolic regulation in Tibetan pigs at high altitude and provide important clues regarding the gastrointestinal adaptations of high-altitude animals.