Background The term “metabolically healthy obese (MHO)” denotes a hale and salutary status, yet this connotation has not been validated in children, and may, in fact, be a misnomer. As pertains to obesity, the gut microbiota has garnered attention as conceivably a nosogenic or, on the other hand, protective participator.Objective This study explored the characteristics of the fecal microbiota of obese Chinese children and adolescents of disparate metabolic status, and the associations between their gut microbiota and circulating proinflammatory factors, such as IL-6 and TNF-α, and a cytokine up-regulator and mediator, leptin. Results Based on weight and metabolic status, the 86 Chinese children (ages 5-15 years) were divided into three groups: metabolically healthy obese (MHO, n=42), metabolic unhealthy obesity (MUO, n=23), and healthy normal weight controls (Con, n=21). In the MUO subjects, the phylum Tenericutes, as well as the alpha and beta diversity, were significantly reduced compared with the controls. Furthermore, Phylum Synergistetes and genus Bacteroides were more prevalent in the MHO population compared with controls. For the MHO subgroup, Spearman’s correlation analysis revealed that serum IL-6 positively correlated with genus Paraprevotella, and leptin correlated positively with genus Phascolarctobacterium and negatively with genus Dialister (all p<0.05).Conclusion Dysbiosis of gut microsystem prevails in the MHO cohort, and the abundance of some metabolism-related bacteria associates with the degree of circulating inflammatory compounds. As for a role in the etiology or facilitation of obesity- or perhaps vice versa- this childhood microbial imbalance awaits long-term, longitudinal investigation.