Overuse of antibiotics in aquaculture, husbandry and healthcare has led to antibiotics residues in the enviuronment and the generation of antibiotic resistant bacteria that can be transferred into the human gut through food chain. Based on literatures, we reviewed the influence of bacterial resistance on intestinal flora and related immune regulation. Taking the source of antibiotic resistance to human intestinal flora as an entry point, we addressed the structure of human intestinal flora and the composition of drug resistance genes after exposure to pollutants. Moreover, we discussed the relationship among changes of intestinal flora, antibiotic resistance genes and immunomodulation related diseases. Last, we also indicated future research needs.