Magnolia officinalisbark is a traditional Chinese medicine for gastrointestinal tract disorders. In this study, we explored the effects ofM. officinalisextraction on intestinal flora to reveal its mechanism. Thirty SPF mice were divided into five groups: C (control),M(M. officinalis), A (antibiotics: cefradine and gentamicin sulfate), A&M(antibiotics + M. officinalis) and A&N (antibiotics + natural recovery). Faecal samples of all groups were collected and the taxonomic composition and diversity of bacteria was characterized using the 16S rRNA gene (16S). Alpha diversity showed gut bacteria diversity significantly decreased in the A group of mice but increased markedly after administration ofM. officinalisextract. Beta diversity indicated that C, M and A&Mshared similar bacterial community structure while A and A&N exhibited a different bacterial community. Furthermore, RDA combined with spearman correlation heatmap suggested the five physiological indicators (weight, fur, activity and feces) were highly correlated with bacterial community structure and diversity. Finally, functional categorization of the assigned OTUs was performed using the PICRUSt tool. The changes in PICRUSt inferred that function profile and metabolic pathways were observed in A and A&M, therefore theM. officinalisextract improved the intestinal flora of A&Mand normalized its metabolic pathways gradually, improving mouse weight, fur quality, activity and feces qualities.