Compound traditional Chinese medicine is one of the medication characteristics of traditional Chinese medicine, as well as its essence. Intestinal microbiotia have a crucial effect on hosts' metabolic function and life activities. Intestinal microbiotia are devoted to dissolution and transformation of the Chinese herbal medicinal ingredients by hydrolysis and restoring reaction. In order to investigate the microecological mechanisms for ultra-micro Qiweibaizhusan on diarrheal mice with intestinal dysbacteriosis, the mouse model with dysbacteriosis was constructed by intragastric administration with antibiotics mixture composed of cefradine capsules and gentamycin sulfate injection. One group of diarrheal mice were treated with the traditional decoction of Qiweibaizhusan, the other group of diarrheal mice were given 1/2 dose of ultra-micro powder Qiweibaishusan, and the normal group and the diarrheal group mice were treated with sterilized water by intragastric administration. After three days' treatment, the intestinal microbiotia were extracted, and their carbon metabolisms were determined by Biolog Microbial Identification System. The results showed that all groups of average of wall color development (AWCD) tended to be stable throughout 72 h cultivation period, but AWCD of the 1/2 dose of ultra-micro powder group > the normal group > the traditional decoction group > the model group. The microbial diversity index, including Shannon index and Simpson index, in the normal group were the largest, and there were significant differences compared with that in other groups (P<0.01). The Shannon evenness and Mclntosh index of the 1/2 dose of ultra-micro powder treated group were very significantly different compared to that of other group (P<0.01, P<0.05), except that the Shannon evenness wasn't significantly different compared with that of the normal group (P>0.05). The results of clustering analysis and principal components analysis suggest that bacteriostasis function of antibiotics was prominent, and some metabolic pathways of intestinal microbiotia in mice were influenced. The metabolic diversity of intestinal microbiotia in mice was gradually regained by the regulatory functions of 1/2 dose of ultra-micro powder and traditional decoction of Qiweibaishusan. There were differences in the regulatory roles of the traditional decoction and ultra-micro powder decoction. The regulatory role of 1/2 dose of ultra-micro powder was more notable than that of traditional decoction. The ultra-micro Qiweibaizhusan had a prominent regulatory role on metabolic diversity of intestinal anaerobic microbiotia in mice, and had a good treatment effect on diarrhea with intestinal dysbacteriosis.