Altered metabonomics and gut microbial dysbiosis have been involved in the pathogenesis of Crohn’s disease (CD). A study aimed to define the structure of the gut microbiome and all the metabolic actions in pediatric Cd patients along with different clinical results after infliximab therapy (IFX). A fecal sample was gathered from 29 lately diagnosed pediatric CD patients and 20 fit and healthy children. 16S rRNA/ITS2 gene-targeted and sequencing metabolic analyses were referred to the profile of the gut bacterial microbiome, mycobiome, and metabolome respectively. Pediatric Cd patients showed lower relative abundances of short-chain fatty acids (SCFAs) generating bacteria including fecal bacterium, ruminococcus, roseburia, and clostridium clusters IV and XIVb, which were associated with reduced fecal levels of SCFAs. Reduced unconjugated bile acids (BAs) pool size and a bit lower conjugated and unconjugated BAs proportion were related to the relative abundance of Clostridium IV and XIVb and Bifidobacterium which includes bile salt hydrolases (BSH) gene. IFX treatment enhanced the BSH-generating bacteria in CD subjects, which might clarify reducing the level of conjugated BAs and increasing unconjugated BAs with the conjugated/ unconjugated BAs ratio. Moreover, a sustained response (SR) of IFX therapy was related to a higher abundance of sphingomonas, streptococcus, methylobacterium, and staphylococcus and a higher fecal concentration of linoleic acid, amino acids, L-aspartic acid, and L-lactic acid at baseline. The study recommended that the results of IFX might be somewhat mediated by improving bacterial taxa that generate SCFAs and BSH thereby inhibiting inflammation while rebuilding the Ba metabolism. Some metabolites and fecal bacteria may be predictive of the results of IFC therapy for pediatric CD.