Objective： To explore the regulatory effect of whey protein and pea protein on mice with intestinal flora disorder， and to reveal the application potential of whey protein and pea protein in regulating intestinal flora disorder. Methods： By infusing lincomycin hydrochloride into mice to establish a model of intestinal flora disorder， intervene in gavage protein samples from model mice， after the intervention， the content of Enterococci， Escherichia coli， Lactobacillus， and Bifidobacterium in the contents of the cecum of the mice was detected， and the colonization resistance of the intestinal microorganisms of the mice was evaluated. Bacterial genomic DNA were collected from fresh feces of each group of mice for 16S rDNA sequencing analysis to evaluate the effect of different samples on the intestinal flora. Results： Compared with the model group， the colonization resistance and species richness of intestinal flora of mice were improved in each treatment group， changed the composition structure of the bacterial community， reduced the number of pathogenic bacteria， promoted the proliferation of beneficial or neutral bacteria， and improved the functional gene composition of the bacterial community. The species composition and functional gene composition of the intestinal flora of mice in each treatment group tended to be at the level of the blank group. Conclusion： Whey protein， pea protein， and pea hydrolyzed protein-peptide can regulate the structure of intestinal flora and improve the disorder of intestinal flora caused by antibiotics.