Ziyuglycoside II (ZGS II) is a major bioactive ingredient of Sanguisorbae officinalis L., which has been widely used for managing myelosuppression or leukopenia induced by chemotherapy or radiotherapy. In the current study, we investigated the pro-hematopoietic effects and underlying mechanisms of ZGS II in cyclophosphamide-induced leukopenia in mice. The results showed that ZGS II significantly increased the number of total white blood cells and neutrophils in the peripheral blood. Flow cytometry analysis also showed a significant increase in the number of nucleated cells and hematopoietic stem and progenitor cells (HSPCs) including ST-HSCs, MPPs, and GMPs, and enhanced HSPC proliferation in ZGS II treated mice. The RNA-sequencing analysis demonstrated that ZGS II effectively regulated cell differentiation, immune system processes, and hematopoietic system-related pathways related to extracellular matrix (ECM)-receptor interaction, focal adhesion, hematopoietic cell lineage, cytokine-cytokine receptor interaction, the NOD-like receptor signaling pathway, and the osteoclast differentiation pathway. Moreover, ZGS II treatment altered the differentially expressed genes (DEGs) with known functions in HSPC differentiation and mobilization (Cxcl12, Col1a2, and Sparc) and the surface markers of neutrophilic precursors or neutrophils (Ngp and CD177). Collectively, these data suggest that ZGS II protected against chemotherapy-induced leukopenia by regulating HSPC proliferation and differentiation.