To investigate the regulatory effects of Sanghuangporus vaninii polysaccharides (SVP) and Sanghuangporus sanghuang polysaccharides (SSP) on the intestinal microbiota in normal organisms (including human beings), a systematic analysis of the intestinal flora of healthy mice was conducted through animal feeding experiments combined with high-throughput sequencing of microorganisms. Thirty mice were randomly divided into control, SVP, and SSP groups, with the SVP and SSP groups being further subdivided into low-dose and high-dose subgroups (administered 200 and 400 mg•kg-1•d via gavage, respectively). SVP and SSP did not significantly affect the growth status, body weight, and thymus coefficient of mice; however they significantly reduced the spleen coefficient (P<0.05). The results from high-throughput sequencing analysis on microorganisms in mice feces revealed that both SSP and SVP significantly reduced the ratio of Firmicutes to Bacteroidetes in the intestinal tract (both decreased by more than 55% compared with CK14). The abundance of the Alistipes was significantly increased by SSP (compared with CK14, increased by 59.25% and 65.62% in SL14 and SH14, respectively). The abundance of Verrucomicrobia and Muribaculum was enhanced in both SVP- and SSP-treated groups, suggesting the potential resistance to SVP- and SSP-mediated metabolic diseases. Heatmap and hierarchical clustering analysis demonstrated that the primary factor influencing the intestinal microbiota of mice was the dosage rather than the type of Sanghuangporus spp. polysaccharides, concluding that both SVP and SSP could have beneficial effects on the intestinal flora, and thereby provide a theoretical foundation for the application of Sanghuangporus spp. in functional foods and health-care products.