[Background] Shenchi was obtained through co-fermentation with the soybean (Glycine max (L.) Merr.), Ginseng (Panax Ginseng C.A.Mey.), and the fermentation probiotics (Bacillus subtilis subsp. subtilis), that was obtianed from the Sojae Semen Praepartaum in our laborary. It has obvious regulation effect on blood index of rats with qi deficiency and blood stasis, and the effect on intestinal micro-ecology is still unclear. [Objective] In order to investigate the effection, that the intestinal micro-ecology for Shenchi on of rats with qi deficiency and blood stasis. [Methods] The rat model of qi deficiency and blood stasis was constructed by the method, that was “exhaustive swimming+restricted diet” with a long-term. Animal models were treated with the high, medium and low doses of Shenchi and Buyang Huanwu Decoction by intragastric administration for 60 days. After 60 days’ treatment, analyzed change in the number of six resident bacteria; and the carbon sources metabolism was determined by Biolog-ECO microbial identification system. [Results] The results showed that the Shenchi could promote the proliferation of beneficial bacteria including Bacteroides fragilis, Lactobacillus and Bifidobacterium in the intestinal flora of rats with qi deficiency and blood stasis, the shenchi could regulate the number of Enterobacter and Enterococci to normal levels, and inhibit proliferation of Clostridium perfringens. Biolog results showed the AWCD value of the high dose group, which was similar to the normal group. At 48 h cultivation period, the value of Shannon index, Shannon evenness, Simpson index and Mclntosh index were significantly higher in the model group than in the normal group, (P<0.05 or P<0.01). The Shannon index, Shannon evenness, and Simpson index of the high-dose group were similar to the normal group (P>0.05), and the values were significantly difference compared with the model group (P<0.01). Cluster analysis and principal component analysis showed that different dose groups of Shenchi were distinct from the normal group, model group and Buyang Huanwu Decoction group, which may be related to the regulation of intestinal microbes in rats with qi deficiency and blood stasis. [Conclusion] Shenchi had a significant improvement on the intestinal flora of rats with qi deficiency and blood stasis.