ABSTRACT: Background: Hepatocellular carcinoma (HCC) remains a global health challenge with limited treatment options and frequent development of drug resistance. Sophora flavescens, a traditional Chinese medicine, contains prenylated flavonoids with documented antitumor potential, though their in vivo efficacy and precise molecular mechanisms against HCC remain largely unexplored. Purpose: This study aimed to systematically evaluate the anti-HCC activity of prenylated flavonoids in S. flavescens (PFS), identify the key bioactive constituents, and elucidate the underlying molecular mechanisms. Methods: The chemical profile of PFS extract was characterized using UHPLC-QE-Orbitrap MS. Anti-HCC effects were assessed in vitro through cell viability, proliferation, migration, cell cycle, apoptosis, and mitochondrial function assays. An in vivo HepG2 cell-derived xenograft model was employed to evaluate tumor growth inhibition and safety. Mechanistic insights were gained via proteomics, western blotting, and in silico analysis. Results: Forty-one prenylated flavonoids were identified in the extract. PFS significantly inhibited HCC cell proliferation and migration, induced cell cycle arrest, apoptosis, and mitochondrial dysfunction in vitro, and suppressed tumor growth in vivo with a favorable safety profile. Proteomic and Western blot analyses revealed that PFS mediates mitochondrial apoptosis by downregulating p-Akt and p-MDM2, upregulating p53 and NOXA, disrupting the Bax/Bcl-2 balance, and activating the cytochrome c/Caspase-3/PARP1 cascade. In silico analysis further suggested C8-prenylated flavonoids, notably (2R,3R)-5-Methoxy-7,4'-dihydroxy-8-[3,3-dimethylallyl]-flavanonol (17), Kushenol M (33), and 2'-methoxy kushenol I (34), might be the key active components targeting the Akt/MDM2/p53 pathway. Conclusion: This study demonstrates that PFS inhibit HCC growth by inducing mitochondrial apoptosis via suppression of the Akt/MDM2/p53 signaling pathway. PFS represents a promising candidate for further development as a complementary therapy for HCC.