The purpose of the study was to investigate the effects of dietary fructooligosaccharide (FOS) on growth performance, biochemical indexes, intestinal morphology, and growth-related gene expression of blunt snout bream (Megalobrama amblycephala) infected by Aeromonas hydrophila (AH). Two hundred twenty-five healthy blunt snout bream with an initial body weight of 38.41 ± 0.88g were randomly divided into five groups with three replicates: control (basal diet), model (AH + basal diet), SFOS (AH + 2g/kg FOS), MFOS (AH + 4g/kg FOS), LFOS (AH + 6g/kg FOS). After 9weeks of feeding, the results showed that the FOS-added diet abrogated AH-induced retardation, hemorrhage, and inflammatory infiltration. FOS supplementation enhanced the growth performance degradation caused by AH, and the highest growth performance was observed at MFOS. Meanwhile, the addition of FOS to feed improved the blood immunity reduced by AH. In expansion, the mucosal epithelium of intestinal villi exfoliated, exposing the lamina propria, and a few villi were genuinely harmed in the model group. Fish fed with MFOS ameliorated the damaged intestine, evidenced by well-preserved intestine architecture. Furthermore, the model group downregulated the expression of growth-related genes (growth hormone receptor (GHR), insulin-like growth factor 1 (IGF-1)). Fish fed with 2g/kg or 4g/kg FOS upregulated the genes specified above expressions in the liver compared with the model group. In conclusion, the results mentioned above suggested that the dietary FOS could relieve the pressure to elevate the immune damage and intestine injury induced by AH and enhance the hepatic expression of IGF-1 and GHR.