[Objective] To verify if a corn-rich diet could change mice gut microbiota structure and enhance the host carbohydrate metabolism related gut flora genes by using high-throughput sequencing. [Methods] We fed mice for 10 weeks with either normal feedstuff or corn-rich feedstuff (containing 1/4 corn and 3/4 normal feedstuff), and compared the gut microbiome changes by high-throughput sequencing of fecal DNA. [Results] Mice in the two diet groups showed similar body weight after 10 weeks feeding. Fecal DNA of all mice generated high efficiency results, and different diet caused diversity difference of gut flora. The abundances of Bifidobacteriales-B. pseudolongum branch and Coriobacteriia-Collinsella/Enterorhabdus branch under Actinobacteria phylum were significantly higher in corn-rich diet group. Correspondingly, the abundances of phosphoglycerate mutase gene, and functional pathways and modules, including primary and secondary bile acid biosynthesis, as well as glucose transfer to pyruvate module and core module involving three-carbon compounds, were also increased in corn-rich diet group. [Conclusion] Corn-rich diet could promote the abundances of probiotics such as Bifidobacterium in gut microbiota, and raise glucose/lipid metabolic related gene and pathway abundances in microbiome, such influence could potentially improve the host metabolism status.