Polyphyllin I (PPI), also called Chong Lou saponin I, is a steroidal saponin isolated from the rhizome of Paris polyphylla. PPI has been demonstrated to have strong anticancer activity. However, its effect on the stemness of liver cancer stem cells (LCSCs) is not completely understood. Herein, we aimed to investigate the effect of PPI on the stem cell-like features of LCSCs and hepatocellular carcinoma (HCC). LCSCs were enriched in a serum-free medium and treated with PPI, sorafenib (Sora), or PPI and Sora. Several endpoints, including spheroid formation and differentiation, cell proliferation, surface markers of LCSCs, PPI binding targets, and stemness-associated protein expression, were evaluated. Immunofluorescence staining, quantitative real-time polymerase chain reaction, siRNA transfection, and coimmunoprecipitation ubiquitination assays were conducted for in-depth mechanistic studies. Evaluation of in vivo antitumor efficacy demonstrated that PPI effectively inhibited the proliferation of liver cancer cells and the self-renewal and differentiation of LCSCs. Flow cytometry indicated that PPI suppressed the expression of the stem cell surface markers EpCAM and CD13. Molecular docking showed a high affinity between PPI and proteins of the Wnt/β-catenin signaling pathway, including AKT, GSK-3β, and β-catenin, with the binding energies of -5.51, -5.32, and -5.40 kcal/mol, respectively, which suggested that PPI might regulate the Wnt/β-catenin signaling pathway to affect the stem cell-like properties of HCC. Further ex vivo experiments implied that PPI activated the AKT/GSK-3β-mediated ubiquitin proteasomal degradation of β-catenin and subsequently attenuated the prooncogenic effect of LCSCs. Finally, the anticancer property of PPI was confirmed in vivo. It was found that PPI inhibited the tumor growth in an HCC cell line xenograft model. Taken together, molecular docking analysis and experimental data highlighted the novel function of PPI in suppressing the stem cell-like characteristics of LCSCs via the AKT/GSK-3β/β-catenin signaling pathway.