A growing body of evidence suggests that the disturbance of intestinal microbiota induced by high-fat diet is the main factor causing many diseases. Dendrobium officinale (DO), a medicinal and edible homologous Chinese herbal medicine, plays essential role in regulating intestinal microbiota. However, the extent of DO on the intestinal contents microbiota in mice fed with a high-fat diet still remains unclear. Therefore, this study explored the role of intestinal contents microbiota in the regulation of adverse effects caused by high-fat diet by DO from the perspective of intestinal microecology. Twenty-four mice were randomly distributed into the normal saline-treated basal diet (bcn), normal saline-treated high-fat diet (bmn), 2.37 g kg−1 days−1 DO traditional decoction-treated high-fat diet (bdn) and 1.19 g kg−1 days−1 lipid-lowering decoction-treated high-fat diet (bjn) groups for 40 days. Subsequently, we assessed the changes in body weight, serum total cholesterol (TC), total triacylglycerol (TG), low density lipoprotein-cholesterol (LDL-C), high density lipoprotein-cholesterol (HDL-C) levels, and the characteristics of intestinal contents microbiota. Results demonstrated that DO exerted the modulating effect on the changes in body weight, TG, TC, LDL-C, and HDL-C levels. Besides, DO decreased the richness and diversity of intestinal contents microbiota, and altered the structure as a whole. Dominant bacteria, Ruminococcus and Oscillospira, varied significantly and statistically. Moreover, DO influenced the carbohydrate, amino acid, and energy metabolic functions. Furthermore, Ruminococcus and Oscillospira presented varying degrees of inhibition/promotion of TG, TC, LDL-C, and HDL-C. Consequently, we hypothesized that Ruminococcus and Oscillospira, as dominant bacteria, played key roles in the treatment of diseases associated with a high-fat diet DO.