The preliminary assays indicated that the inhibitory activity against the growth of NCI-H661 decreased in an order of linked chromophore flavone-6-yl 16a–d > flavone-7-yl 17a–d > flavone-3-yl 15a–d and isoflavone-7-yl 18a–d. Among these flavone-6-yl derivatives, N-(4-methoxyphenyl)-2-(4-oxo-2-phenyl-4H-chromen-6-yloxy)acetamide (16c) was the most potent with a GI50 value of 0.84 μM. The inhibitory activity against the growth of NPC-TW01 decreased in an order of linked chromophore flavone-6-yl 16a–d > isoflavone-7-yl 18a–d > flavone-7-yl 17a–d > flavone-3-yl 15a–d. Flavone-6-yl derivatives 16a–d demonstrated significant inhibitory activities against the growth of NPC-TW01 cell with an average GI50 value of 0.84 μM. The oxime derivatives 1 and 2 caused accumulation of NPC-TW01 cell in G2/M phase which were distinct from that of their amide isomers 16b and 16c, respectively, which induced cell-cycle arrest in G0/G1 phase followed by apoptosis. Therefore, the antiproliferative mechanism of flavone derivatives was affected not only by the phenyl benzopyran-4-one pharmacophore but also by the peripheral substituents.