The main aim of this study was conducted to evaluate the effect of chronic exposure to low concentrations of deltamethrin on the Carassius auratus gibelio by molecular biological analysis. In brief, the histopathological analysis of the intestinal tract was implemented, and the intestinal villi length, muscular layer thickness, and the number of mucus cells were measured to imply intestinal health in fish. Furthermore, the expression of the intestine barrier, oxidative stress, inflammatory response, apoptosis, and autophagy-related genes was quantified. And then, the 16S rRNA sequencing was performed to reveal the change in the intestine microbiota composition. To sum up, our results will provide a brand-new perspective of deltamethrin toxicity on intestine health and explore the potential link between intestine microbiota and physiological status.