Background Cyclin-dependent kinases 2/4/6 (CDK2/4/6) play critical roles in cell cycle progression, and their deregulations are hallmarks of hepatocellular carcinoma (HCC).Methods Here we combined computational and experimental approaches to discover a CDK2/4/6 triple-inhibitor from FDA approved small-molecule drugs for the treatment of HCC.Results Based on molecular docking results, vanoxerine dihydrochloride was found to exhibit strongest cytotoxic effect on human HCC QGY7703 and Huh7 cells (IC50: 3.79 µM for QGY7703and 4.04 µM for Huh7 cells). Vanoxerine dihydrochloride treatment caused G1arrest, induced apoptosis, and reduced the expressions of CDK2/4/6, cyclin D/E, retinoblastoma protein (Rb), as well as the phosphorylation of CDK2/4/6 and Rb in QGY7703 and Huh7 cells. In addition, combined vanoxerine dihydrochloride and 5-Fu produced synergistic cytotoxicity in Huh7 cells. Finally, in vivo studies in preclinical animal model of BALB/C mice subcutaneously xenografted with Huh7 cells, we showed that injection of vanoxerine dihydrochloride (40 mg/kg, i.p.) produced significant antitumor activity (p < 0.05), comparable to that achieved by 5-Fu (10 mg/kg, i.p.), with the combination treatment resulted in strongest effect.Conclusions The present study is the first to identify a CDK2/4/6 triple inhibitor vanoxerine dihydrochloride, and demonstrate that it represents a novel therapeutic strategy for HCC treatment alone or in combination with 5-Fu.