Jian-Pi-Yi-Shen (JPYS) is one of the herbal medicines for treatment of anemic patients with chronic kidney disease (CKD). However, less of scientific evidence to support JPYS involved in treating anemia has been revealed. Here, an animal study was performed to investigate its hematopoietic activities and the underlying mechanism. The 5/6 nephrectomized inductions of CKD anemic rats were randomly divided into two groups: CKD group and JPYS group. Sham-operated rats served as sham group. JPYS (1.36 g/kg/d) was administered orally to CKD rats daily for six consecutive weeks. Results showed that JPYS treatment notably improved renal function and pathological injury in CKD rats. JPYS also restored the hematological parameters, including red blood cells, hemoglobin, and hematocrit. In parallel, the reduction level of EPO was reversed by JPYS. Furthermore, JPYS induced the accumulation of hypoxia inducible factor (HIF)-α protein expression. Collectively, these results provide convincing evidence for JPYS decoction in ameliorating CKD-associated anemia, and its mechanism might be related to regulate EPO production via HIF signaling pathway.