This study aimed to systematically evaluate the anti-tumor efficacy of petroleum ether, ethyl acetate (EAE), and water extracts from Sanghuangporus mongolicus and decipher the molecular mechanisms of the most efficacious extract - EAE. Using H22 tumor-bearing mice, high-dose EAE (37.72 mg/kg) exhibited the highest tumor inhibition rate (75.14 %) without toxicity. Histopathology examination demonstrated that EAE effectively mitigated tumor progression and multi-organ damage, whereas ELISA and serum biochemical assays indicated modulated levels of immune mediators (IL-6, IL-2, IFN-γ, TNF-α, and VEGF) and restored serum levels of hepatic (ALT, AST) and renal (BUN, Cr, UA) functional markers. Integrated transcriptomics and metabolomics demonstrated that EAE suppressed tumor growth via multi-target regulation involving immune responses, biosynthesis of amino acids, and mitochondrial apoptosis pathways. Western blotting validated EAE upregulated pro-apoptotic cleaved caspase-3, caspase-3, Bax, and TNF-α (p < 0.01 vs. model group (MG)), upregulated immune-related protein JCHAIN, MZB1 (p < 0.01 vs. MG), downregulated anti-apoptotic Bcl-2 (p < 0.01 vs. MG). LC-MS identified 33 EAE compounds, with 32 showing strong binding (ΔG ≤ -5.0 kcal/mol) to core targets, JCHAIN and MZB1, via molecular docking. Phellibaumin C, inoscavin A, and phelligridin D exhibited the highest binding affinities. This study provides a multi-target mechanistic framework for developing S. mongolicus EAE as a natural anti-hepatocellular carcinoma (HCC) agent.