[Background] Gut microbiota is an important part of human body and plays an important role in various life activities. [Objective] To explore the characteristics of gut bacteria community in Uyghur and Han children in order to provide more effective and accurate nutrition intervention strategies for children's nutritional health monitoring and nutrition improvement. [Methods] 20 children of 10?12 years of school age Uyghur and Han nationality were selected from Zepu county and Minquan county, respectively. Collect their fresh feces at the same time period, extracted the total bacterial DNA, through high-throughput sequencing and bioinformatics analysis to study the gut bacteria community differences between healthy Uyghur children and Han children. [Results] 2 007 100 sequences were obtained and classified into 994 OTUs. All the samples contained a total of 15 phyla and 139 genera. Alpha and Beta analyses indicated that there were statistically significant differences in the richness and diversity of gut bacteria in children of the two ethnic groups in the surveyed regions. The richness of gut bacteria community in Uyghur children was higher than that in Han children, while the species diversity was lower than that in Han children. The dominant phyla and genera of Uyghur children's gut bacteria are Bacteroidetes (63%), Firmicutes (22%), Prevotella (61%), Succinivibrio (9%) and Faecalibacterium (5%). While in Han children, the dominant phyla and genera are Firmicutes (57%), Bacteroidetes (23%), Faecalibacterium (16%), Prevotella (11%) and Bacteroides (11%). [Conclusion] The significant differences of gut bacteria community between Uyghur and Han children in the surveyed regions provide a scientific basis for further research on the relationship between gut microbiota, dietary factors and human nutritional health.