[Objective] The intestinal tract comprises the main digestive organs of animals and is an important barrier that confers organism resistance to exogenous pathogens. The intestinal flora of animals is reportedly related to animal species, feeding methods and growth stage. However, it is unclear whether the intestinal bacteria of house-feeding Tibetan, grazing Tibetan and Landrace, York and Duroc (DLY) three-way hybrid pigs differ. [Methods] The intestinal tissues of 6-month-old to 7-month-old grazing Tibetan, house-feeding Tibetan and DLY pigs were selected. The intestinal morphology of each pig was determined by tissue section method. The digestive enzyme activity of intestinal contents was determined by using an enzyme activity assay kit. The intestinal microbiota was examined through high-throughput sequencing technology. [Results] The muscular thickness and villus height of duodenum, jejunum and ileum of DLY pigs were significantly higher than those of Tibetan pigs. The crypt depth of the duodenum, jejunum and ileum of DLY pigs was significantly lower than that of Tibetan pigs. The intestinal morphology was not significantly different between grazing and house-feeding Tibetan pigs. The trypsin activity in the small intestines of DLY pigs was remarkably higher than that of Tibetan pigs, whereas the amylase activity in the small intestines of DLY pigs was noticeably lower than that of Tibetan pigs. The dominant phyla in all three groups were Proteobacteria, Firmicutes and Bacteroidetes. The dominant genera in Tibetan pigs were Ralstonia and Escherichia, whereas the dominant genera in DLY pigs were Ralstonia and Bradyrhizobium, but the contents were significantly different. The similarity of the intestinal bacterial community structure between house-feeding and grazing Tibetan pigs was higher than that between Tibetan and DLY pigs. [Conclusion] Significant differences in intestinal morphology, digestive enzyme activity and intestinal microbial structure were observed among grazing Tibetan, house-feeding Tibetan and DLY pigs.