The intestinal flora disturbance animal model was established by intraperitoneal injection of lincomycin hydrochloride to mice. The effect of fermented pea peptide on the structure and diversity of intestinal bacteria was determined based on 16s rRNA amplicon sequencing technology， and the protective effect on intestinal mucosa was investigated by HE staining of the colon of mice. The groups of pea protein， pea peptide and enzymatic pea protein powder with or without probiotics were set up to further explore the advantages of fermented pea peptide in regulating the structure and diversity of intestinal flora. The results show that lincomycin hydrochloride reduced the diversity and richness of intestinal flora in mice accompanied by an increase in the proportion of firmicutes and bacteroides. Moreover， the colonic mucosa of the mice was severely damaged， and the number of goblet cells decreased so that the mucosal barrier was destroyed. Fermentation of pea peptide could increase the species diversity and richness of intestinal bacteria， and when the intragastric dose was 1.6 g/kg， fecal flora diversity was most similar to that of the control group. In addition， HE staining results showed that fermentation pea peptide could increase the number of goblet cells， reduce the infiltration of inflammatory cells， and have a good protective effect on the colonic mucosa. Therefore， fermented pea peptide has a certain role in regulating the composition of intestinal flora.