[Background] Intestinal microbiota is related to several physiological functions of human body. A large number of studies have shown that Qiweibaizhu powder has effects on diarrhea mice. [Objective] Compare with traditional Chinese medicine and ultra-shattered medicine curative effect. To explore the correlation efficacy with Qiweibaizhu powder to provide scientific evidence for the clinical application. [Methods] Dysbacteriotic diarrheal mice model were constructed via administration of antibiotics and then treated with traditional Qiweibaizhu powder and 50% amount of ultra-shattered Qiweibaizhu powder. After the treatment, 16S rRNA gene of microorganisms in intestinal contents of different groups was analyzed by PCR cloning, and corresponding gene library was constructed. [Results] Lactobacillus spp., Enterococcus feacium, Clostridium spp., Blautia producta, Anaerostipes spp., Staphylococcus saprophyticus and uncultured bacterium were in the normal intestinal microbial flora, and Lactobacillus spp. was the dominant bacteria in the predominant intestinal microbial flora, accounting for 61.90% of the total bacterial DNA clone number. Compared with the control group, the proportion of Lactobacillus spp. in the model group was significantly decreased and opportunistic pathogen was increased. After intrgastric administration, the proportion of Lactobacillus spp. in the traditional Qiweibaizhu powder treatment group and 50% amount of ultra-shattered Qiweibaizhu powder treatment group was recovered, which the proportion of Lactobacillus spp. in 50% amount of ultra-shattered Qiweibaizhu powder treatment group was close to the normal group. Through establishing a clustering tree and calculating the diversity (H), species richness (S) and dominance index (D) of each category, we knew that each index of 50% amount of ultra-shattered Qiweibaizhu powder treatment group were approximately to the control group. In conclusion, the intestine microbial diversity of 50% amount of ultra-shattered Qiweibaizhu powder treatment group was most close to the normal group. [Conclusion] The 16S rRNA gene clone library technique was used to further clarify the composition of bacterial community in normal mice and the recovery of intestinal bacterial community in Qiweibaizhu powder, and the effect of 50% amount of ultra-shattered Qiweibaizhu powder treatment was better than the traditional Qiweibaizhu powder treatment.