Irradiation technology can improve the biological activities of natural molecules through a structural modification. This study was conducted to investigate the enhancement of the anticancer effects of chrysin upon exposure to gamma irradiation. Gamma irradiation induces the production of new radiolytic peaks simultaneously with the decrease of the chrysin peak, which increases the cytotoxicity in HT-29 human colon cancer cells. An isolated chrysin derivative (CM1) exhibited a stronger apoptotic effect in HT-29 cells than intact chrysin. The apoptotic characteristics induced by CM1 in HT-29 cells was mediated through the intrinsic signaling pathway, including the excessive production of included reactive oxygen species, the dissipation of the mitochondrial membrane potential, regulation of the B cell lymphoma-2 family, activation of caspase-9, 3, and cleavage of poly (adenosine diphosphate-ribose) polymerase. Our findings suggest that CM1 can be a potential anticancer candidate for the treatment of colon cancer.