Radix Astragali polysaccharide RAP has been reported to play a crucial role in hematopoiesis without a clear mechanism. In this study, RAP's effects to enhance the recovery of cyclophosphamide (Cy)-suppressed bone marrow and blood cells is confirmed in vivo first. Confocal micrographs demonstrated the interesting direct binding of FITC-RAP to hematopoietic stem cells (HSC) in bone marrow. RAP protects both mice and human HSC in terms of cell morphology, proliferation, and apoptosis. RNA-sequencing and shRNA approaches revealed FOS to be a key regulator in RAP's protection. These evidences provide an unreported mechanism that RAP directly protects hematopoietic stem cells from chemotherapy-induced myelosuppression by increasing FOS expression.