This study takes two wild mammals living in the same environment, but with different evolutionary relationships and different dietary habits (Apodemus, Erinaceidae and Soricidae) as the research objects, using the 16S rRNA gene amplicon sequencing technology to analyze and compare the gut microbiota of these mammals. 5378 operational taxonomic units (OTU) are identified, mainly affiliated with Firmicutes (40.55%), Proteobacteria (34.60%), and Bacteroidetes (13.67%). Firmicutes and Bacteroidetes are the dominant phyla of the Apodemus. Proteobacteria is the dominant phylum of Erinaceidae and Soricidae. The results of diversity analyses show that the gut microbiota diversity and community composition are significantly different among Apodemus, Erinaceidae and Soricidae. LEfSe analysis shows that there are more bacteria related to complex carbohydrate fermentation in the Apodemus, while the Erinaceidae and Soricidae contains higher amino acid fermentation bacteria. Probiotics, such as Lactobacillus and Lactococcus, coexist in these three wild small mammals to regulate host health. This study reveals that phylogeny and feeding habits of the host have a profound effect on the shaping gut microbes. The gut microbiota may also play a probiotic effect on the host in many aspects.