Hepatocellular carcinoma (HCC) is a common type of cancer—prevalent worldwide—and one of the causes of cancer-related deaths. In this study, ethanol extracts from Pholiota adiposa (EPA) were used to identify possible targets for HCC treatment and their effects on intestinal microflora were analyzed. Methods: Male mice were randomly assigned to groups—the model group, cyclophosphamide (25 mg/kg/d), and EPA groups, in which the mice were categorized based on the different concentrations of each compound (100, 200, and 300 mg/kg/day). Relevant biochemical indicators were detected using ELISA, H&E staining, and TUNEL assay. Four tumor apoptosis-related proteins and genes, Caspase3, BAX, Bcl-2, and VEGF, were detected by immunohistochemical staining, western blotting, and RT-PCR. The total genomic DNA was obtained from the contents of the small intestine and colon and was sequenced. The V3+V4 regions of bacterial 16s rDNA (from 341 to 806) were amplified. Results: The tests revealed that EPA exhibited antitumor activity in vivo by promoting apoptosis and inhibiting angiogenesis. Moreover, EPA treatment could increase beneficial and decrease harmful microflorae. These results demonstrate that EPA may be a potential therapy for HCC.