Objective To investigate the structural characteristics of intestinal flora in children with sepsis and its association with inflammatory response.Methods A prospective cohort study was conducted.The children with sepsis who were admitted from December 2021 to January 2023 were enrolled as the sepsis group,and the children with non-sepsis who were admitted during the same period were enrolled as the non-sepsis group.The two groups were compared in terms of the distribution characteristics of intestinal flora,peripheral white blood cell count(WBC),C reactive protein(CRP),and cytokines,and the correlation of the relative abundance of fecal flora with WBC,CRP,and cytokines was analyzed.Results At the genus level,compared with the non-sepsis group,the sepsis group had significantly lower relative abundance of Akkermansia,Ruminococcus,and Alistipes and significantly higher relative abundance of Enterococcus,Streptococcus,and Staphylococcus(P<0.05).At the phylum level,Proteobacteria was the dominant phylum(37.46%)in the group of children with a score of≤70 from the Pediatric Critical Illness Score(PICS),and Firmicutes was the dominant phylum in the group of children with a score of 71-80 or 81-90 from the PICS(72.20%and 43.88%,respectively).At the genus level,among the 18 specimens,5 had a relative abundance of>50%for a single flora.Compared with the non-sepsis group,the sepsis group had significant higher levels of WBC,CRP,interleukin-6(IL-6),interleukin-10(IL-10),and tumor necrosis factor-α(P<0.05).The Spearman's rank correlation analysis showed that at the genus level,the relative abundance of Ruminococcus,Alistipes,and Parasutterella in the sepsis group was negatively correlated with the levels of WBC,CRP,and IL-6(P<0.05);the relative abundance of Enterococcus was positively correlated with the CRP level(P<0.01);the relative abundance of Streptococcus and Staphylococcus was positively correlated with the levels of CRP and IL-6(P<0.05);the relative abundance of Streptococcus was positively correlated with WBC(P<0.05).Conclusions Intestinal flora disturbance is observed in children with sepsis,and its characteristics vary with the severity of the disease.The structural changes of intestinal flora are correlated with inflammatory response in children with sepsis.