Taking sophoridine as a lead compound, 58 sophoridine derivatives were designed, synthesized and evaluated for their antiproliferative activity in the HepG2 cancer cell line. Among the 58 compounds, 33 compounds showed potent antiproliferative activity with IC50 less than 10 μM. Compound 5w showed the most potent anti-proliferative activity in the HepG2 cancer cell line. Thus, we further extended our characterization of the antiproliferative activity of 5w in six cancer cell lines (HepG2, SMMC-7721, Hela, CNE1, CNE2 and MCF7). The representative compound 5w displayed robust anti-proliferative activities in all the tested cell lines with IC50 values in range of 0.93-1.89 μM which were much lower than that of sophoridine. Here, we report the structure-activity relationships (SAR) in a sophoridine series of compounds, which indicated that introduction of N-benzyl indole group on the 14-carbon atom of sophoridine can significantly enhance the antiproliferative activity. By molecular docking and enzymatic assay, compound 5w was found to be able to inhibit the activity of DNA Topo I. Furthermore, apoptosis assay displayed that compound 5w could significantly induce the apoptosis of HepG2 cells in a dose-dependent manner by activating caspase-3, increasing expression of cleaved caspase-3 and reducing the ratio of Bcl-2/Bax. The in vivo antitumor assay demonstrated that 5w suppressed the growth of HepG2 xenografts in nude mice without any obvious side effects.