Present studies on ethnicity and intestinal flora show that different ethnic factors, such as diet, geography, and genetics, can make remarkable differences in the structure of intestinal microbiota. To the best of our knowledge, in this study, the differences in intestinal flora of healthy Dai and Han Chinese in the Yunnan region of China were determined for the first time by high-throughput sequencing, and the correlation between polymorphisms of FOXC2 C-512T and the structure of intestinal flora was analyzed. The study found that there were significant differences in alpha and beta diversity in intestinal flora between healthy Dai and Han people, and the two ethnic groups had dominant microbiota, through analysis at gate and genus levels. Moreover, our study shows that the intestinal flora structure of FOXC2 C-512T locus CT is different from that of the other two genotypes in terms of alpha and beta diversity and that FOXC2 C-512T polymorphism can affect the composition of human intestinal flora. This study mainly fills the gap in the field of ethnic-gut microbiome research of Dai people and reveals the effect of FOXC2 C-512T polymorphism on the structure of human intestinal flora.