Diets containing different crude protein levels (16%, 14%, and 12%) were created to feed Bamei pigs in order to study the effect of these compositions on intestinal colonies. Therefore, 27 healthy Bamei pigs of similar weight (20.99 kg±0.16 kg) were selected and randomly divided into three groups for microbial diversity analysis. The results of this study show that microbial diversities and abundances in Bamei pig jejunum and caecum samples after feeding with different dietary protein levels were significantly different. Dietary crude protein level exerted no significant effect on the Shannon index for cecum microbes in these pigs, while Simpson, ACE, and Chao1 indices for group I were all significantly higher than those of either the control group or group II (P < 0.05). Indeed, data show that microbial diversities and abundances in the 14% protein level group were higher than those in either the 16% or 12% groups. Dominant bacteria present in jejunum and cecum samples given low-protein diets were members of the phyla Firmicutes and Bacteroidetes. Data show that as dietary crude protein level decreases, representatives of the microbial flora genus Lactobacillus in jejunum and cecum samples gradually increases. Values for the KEGG functional prediction of microbial flora at different dietary protein levels also shows that genes of jejunum and cecum microorganisms were mainly enriched in the ‘metabolism’ pathway, and indicate that low protein diets increase intestinal metabolic activity. Therefore, we recommend that Bamei pig dietary protein levels are reduced 2% from their existing level of 16% crude protein. We also suggest that essential synthetic amino acids (AA) are added to optimize this ideal protein model as this will increase intestinal flora diversity in these pigs and enhance health. These changes will have a positive effect in promoting the healthy growth of Bamei pigs.