Enhanced P53 signaling may lead to hematopoietic disorders, yet an effective therapeutic strategy is still lacking. Our study, along with previous research, suggests that P53 overactivation and hematopoietic defects are major consequences of zinc deficiency. However, the relationship between these two pathological processes remains unclear. In this study, we observed a severe reduction in the number of hematopoietic stem cells (HSCs) and multi‐lineage progenitor cells in zebrafish treated with the zinc chelator N,N,N′,N′‐tetrakis(2‐pyridylmethyl)ethylenediamine and showed the indispensable role of P53 signaling in the process. Next, we took advantage of HSCs‐labeled transgenic zebrafish and conducted a highly efficient phenotypic screening for small molecules against P53‐dependent hematopoietic disorders. Hydroxysafflor yellow A (HSYA), a natural chalcone glycoside, exhibited potent protection against hematopoietic failure in zinc‐deficient zebrafish and strongly inhibited the P53 pathway. We confirmed the protective effect of HSYA in zinc‐deficient mice bone marrow nucleated cells, which showed a significant suppression of P53 signaling and oxidative stress. Furthermore, the hematopoietic‐protective activity of HSYA was validated using a mice model of myelotoxicity induced by 5‐FU. In summary, our work provides an effective phenotypic screening strategy for identifying hematopoietic‐protective agents and reveals the novel role of HSYA as a promising lead compound in rescuing hematopoietic disorders associated with P53 overactivation.