Abstract: To investigate the effect of Sishen Wan (SSW) on intestinal flora in diarrhea-predominant irritable bowel syndrome (IBS-D) rats and explore the efficacy of this regiment for improving IBS-D, we divided 45 SPF male SD rats randomly into control, disease, SSW, Ershen Wan (ESW) and Wuweizasan (WWZS) groups. The spleen-kidney-yang deficiency type IBS-D rat model was prepared by a composite factor and administered for 14 days. After collecting the feces of the rats, total DNA was extracted from the stool samples. Primers were designed based on the 16S r RNA V3 to V4 regions of the bacteria, and used for high-throughput sequencing with the Illumina Miseq platform. We found that SSW can effectively reduce the diarrhea index (P<0.05) and reduce the high sensitivity of intestinal tract (P<0.05) of IBS-D rats. The principal component analysis (PCA), principal co-ordinates analysis (PCoA) and non-metric multidimensional scale analysis (NMDS) based on the Beta diversity distance showed that there were significant differences in the composition of the gut microbiota among the five groups (P<0.05). The disease group has the lowest in abundance, uniformity and diversity of gut microbiota. Compared with the control group, the disease group showed a significant increase in Proteobacteria, Actinobacteria, Veillonococcus and Mycoplasma (P<0.05), but a significant reduction in Pleaverella (P<0.05). Compared with the disease group, SSW administration caused significant reduction in the Proteobacteria and Mycoplasma (P<0.05), but significant increases of Clostridium, Turicibacter and Romboutsia (P<0.05). Our study shows that SSW has the potential as a therapeutic regiment for treatment of IBS-D due to partial regulation of the intestinal flora. In addition, there is a synergy between ESW and WWZS.