Topoisomerase I inhibitors have been developed for a variety of clinical applications. In the present study, we report the antiproliferative activity of some sulphonic acid esters derived from evodiamine as well as 5-methylene evodiamine, for the purpose of improving therapeutic benefits of evodiamine. The synthesized compounds 3a-3g and 5a-5g were evaluated for their in vitro cytotoxicity against A549, HepG-2, U251, HeLa and MCF-7 human carcinoma cell lines by MTT assay. Compound 3e exhibited potent anti-tumor activities on all cell lines (IC50 ranged between 2.68 μM and 18.42 μM ). Moreover, 3e was found to be able to inhibit substantially the tumor growth on the HepS-bearing mice at a dose of 80 mg/kg. Subsequently, preliminary structure-activity relationship was explored based on the biological data, which could provide guidance for designing new analogues of evodiamine. Finally, molecular modeling studies of sulfonic evodiamine esters revealed that they could form hydrogen-bonding and hydrophobic interactions with several amino acid residues of topoisomerase I, resembling the binding format between camptothecin and topoisomerase I.