This experiment studied the recovery of Streptococcus lactis L16 on mice intestinal flora of Staphylococcus aureus after infection. The 16S rRNA gene sequencing library of mouse intestinal microbiota was constructed by high throughput sequencing technique， the composition and biodiversity of the prevention group， the treatment group， the control group and the model group were analyzed， by the bacterial community structures， rank-abundance distribution curves， heatmaps， rarefaction curve， Venn diagrams. Results： In the model group， the deferribacteres （12.67%） was significantly increased and the flora structure was abnormal. The relative abundance of the main phyla of firmicutes（49.03%） and the bacteroidetes （43.15%） in the prevention group was close to the control group （44.75%， 42.08%）. Conclusion： Streptococcus lactis L16 prevents intestinal infection of Staphylococcus aureus in mice and regulates the structure of intestinal flora.