AbstractA bis‐dimethylamine substituted xanthone (Xan‐2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6‐trihydroxyxanthone (Xan‐1) which was isolated from Polygala hongkongensis Hemsl.. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan‐1 and Xan‐2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan‐2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan‐2 exhibited higher DNA binding affinity than Xan‐1. Further study showed that Xan‐2 could inhibit the proliferation of HeLa, SGC‐7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan‐2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.