A double Claisen rearrangements synthetic strategy was established for the total synthesis of 4,4'-dimethyl medicagenin (compound 6c). A series of its analogs also were prepared, including two novel 3',5'-diprenylated chalcones, in which ring B was replaced by azaheterocycle. The structures of the twenty-two newly synthesized compounds were confirmed by 1H NMR, 13C NMR and ESI-MS. In vitro, the cytotoxicity of the target compounds was evaluated using cancer cells. Noticeably, compound 10 exhibited broad-spectrum cytotoxicity on PC3 prostate cancer cells, MDA-MB-231 breast cancer cells (MDA), HEL and K562 erythroleukemia cells with IC50 values of 2.92, 3.14, 1.85 and 2.64 μM, respectively. Further studies indicated that compound 10 induced apoptosis and arrested the cell cycle phase of the above mentioned four cancer cell lines. By contrast, compound 6g selectively displayed potent inhibitory activity against the proliferation of HEL cells with an IC50 value of 4.35 μM. Compound 6g slightly induced apoptosis and arrested cell cycle phase of HEL cells. Preliminary structure-activity relationship studies indicated that, in all cancer cell lines evaluated, the 3-pyridinyl group was essential for cytotoxicity.