[Objective] We studied the effect of two diets on colonic microbial community structure and metabolites in Huanjiang mini-pigs. [Methods] Ten Huanjiang mini-pigs (initial bodyweight 33.5±8.1 kg) were randomly assigned into 2 groups with 5 pigs each, of which one group was fed with a diet with high-level nutrient (crude protein 13.11%, digestible energy 14.73 MJ/kg), and the other with low-level nutrient (crude protein 9.77%, digestible energy 12.24 MJ/kg). After 75 d, all animals were killed and the samples of colonic content were collected. Total bacterial DNA of three samples of pigs per group was extracted, and used to amplify PCR for 16S rRNA gene V4 tag fragment and sequence using high-throughput Miseq technique. Based on the QIIME platform, the microbial community diversity in colonic content was compared. The contents of short-chain fatty acid, ammonia, bioamine, indole, and skatole in colonic contents from five pigs per group were also analyzed using gas chromatography or liquid chromatography. [Results] Firmicutes, Bacteroidetes, Spirochaetes, and Tenericutes were the dominant phyla in colonic content of Huanjiang mini-pigs; dietary nutrient components did not affect the microbial community diversity in colonic content of Huanjiang mini-pigs. The relative abundance of Euryarchaeota was lower in colonic content of pigs fed diet with high-level nutrient, whereas Ruminococcus and Pseudobutyrivibrio were higher than those fed diet with the low-level nutrient. The contents of acetate and propionate were lower in colonic content of pigs fed diet with high-level nutrient, but ammonia and cadaverine were higher than those fed diet with the low-level nutrient. [Conclusion] Firmicutes, Bacteroidetes, Spirochaetes, and Tenericutes were the dominant phyla in colonic content of Huanjiang mini-pigs; diet with high-level nutrient in short feeding-period altered the contents of several colonic bacteria and their metabolic properties.