The current research tried to investigate the effect of Qiweibaizhu powder (QWBZP) on intestinal mucosa bacterial lactase gene from dysbacterial diarrhea mice, as the good therapeutic mechanism of QWBZP on antibiotics-induced diarrhea. Dysbacterial diarrhea mice model was constructed by gastric perfusion with mixture of cephradine capsules and gentamicin sulfate (23.33 mL kg −1 day −1 ) for 5 days. After the success of establishing diarrhea, the mice in treatment group were gavaged with QWBZP for 3 days. Intestinal mucosa in each group was collected, and diversity of bacterial lactase genes in intestinal mucosa of mice was carried out by Miseq metagenome sequencing. The results showed the Chao1, ACE, Simpson and Shannon indices in treatment group were lower than model group and were similar to control group. The same result was obtained from the operational taxonomic units (OTUs). There were 298, 435 and 254 OTUs in the control group, model group and treatment group, respectively. Principal component analysis (PCA) indicated that samples distribution in both normal and treatment groups were relatively intensive, distances among individuals were small, while opposite results were observed in model group. Moreover, antibiotics increased the diversity and abundance of bacterial lactase genes at phylum and genus levels. However, they decreased and were similar to control group after treating with QWBZP. Our results indicate that QWBZP has a positive effect on the recovery of bacterial lactase gene diversity to normal level. In addition, QWBZP increase the abundance of Lysobacter and Eukaryota.