Ionizing radiation (IR) is known not only to cause acute bone marrow (BM) suppression but also to lead to long-term residual hematopoietic injury. These effects have been attributed to IR inducing the generation of reactive oxygen species (ROS) in hematopoietic cells. In this study, we examined if isorhapontigenin and heyneanol-A, two analogues of resveratrol, could mitigate IR-induced BM suppression. The results of cell viability assays, clonogenic assays, and competitive repopulation assays revealed that treatment with these compounds could protect mice BM mononuclear cells (BMMNC), hematopoietic progenitor cells, and hematopoietic stem cells from IR-induced BM suppression. Moreover, the expression of genes related to the endogenous cellular antioxidant system in hematopoietic cells was analyzed. The expression and activity of SOD2 and GPX1 were found to be decreased in irradiated BMMNC, and the application of the resveratrol analogues could ameliorate this damage. Our results suggest that in comparison with resveratrol and isorhapontigenin, treatment with heyneanol-A can protect hematopoietic cells from IR-induced damage to a greater degree; the protective effects of these compounds are probably the result of their antioxidant properties.