Abstract: This study aims to explore the relationship between intestinal flora and its metabolites of Mongolian obese children. 15 Mongolian obese children were selected as obesity group and 15 Mongolian normal weight children were selected as normal group in Tongliao city of the Inner Mongolia Autonomous Region. The fecal samples of two groups of children were collected, the intestinal microbes were detected by 16S rDNA technique, and the diversity and difference of intestinal flora between the two groups of feces were analyzed. The differential metabolites between the two groups of feces were screened by gaschromatography-mass spectrometry（GC-MS） technology, and the enrichment analysis pathway was predicted. Results showed the abundance of Bacteroides and Firmicutes in feces of obesity group children was lower than that of normal group children（P＜0.05）, while the abundance of Actinobacteria and Proteobacteria of obesity group were higher than that of normal group（P＜0.05）. There were significant differences between obesity group and normal group in 7 common dominant genera（P＜0.05）, among which 4 genera were down-regulated and 3 genera were up-regulated in obesity group. Here were differences among 12 metabolites（P＜0.05）, the contents of 6 metabolites such as tyrosine and tetrahydrocorticosterone decreased, while the contents of 6 metabolites such as ribolactone and 4-Cholesten-3-one increased. After the analysis of differential metabolites enrichment, it was found that the changes of metabolic pathways mainly focused on the phenylalanine, tyrosine and tryptophan biosynthesis. According to the correlation analysis between different bacteria and different metabolites, Alistipes was negatively correlated with 4-Cholesten-3-one, Bacteroides, Ruminococcus and Alistipes with citrulline, Blautia with N-Acetyl-D-mannosamine and ribonolactone, and Pseudobutyrivibrio with 4-Cholesten-3-one were positively correlated. There are differences in the structure of intestinal flora and fecal metabolic spectrum between normal group and obesity group, and there is a correlation between the two. Citrulline, 4-Cholesten-3-one, N-Acetyl-D-mannosamine and ribonolactone and may become biomarkers of obesity in Mongolian children.