This study aimed to prepare icariside I (ICS I) and icariside II (ICS II) from Epimedium koreanum Nakai, explore their protective mechanism against cyclophosphamide-induced bone marrow suppression in mice and determine their regulatory effects on immune function. The results showed that after treatment with ICS I and ICS II, the number of peripheral blood cells in the mice returned to normal. The number of bone marrow nucleated cells (BMNCs) and haematopoietic progenitor cell (HPC) colonies in the ICS I-H and ICS II-H treatment groups increased significantly. The thymus and spleen indices and related cytokine levels in the mice returned to normal. ICS I-H and ICS II-H treatment significantly increased the ratio of Bcl-2/Bax and downregulated the expression of caspase-3 to regulate cell apoptosis. In conclusion, ICS I and ICS II promoted the proliferation and differentiation of bone marrow haematopoietic cells and protected the damaged immune system, and the therapeutic effects of high doses were more significant. Regulating the levels of haematopoietic cytokines, the balance of Bcl-2/Bax, and the inhibition of caspase-3 expression may be the mechanisms of action of ICS I and ICS II against cyclophosphamide-induced bone marrow suppression in mice.