In this study, we aimed to investigate the effects of the combination of Panax ginseng and Ophiopogon japonicus (PG–OJ) herbs at different ratios on myelosuppression induced by chemotherapy. The myelosuppression model was established using an intraperitoneal injection of 100 mg kg−1 cyclophosphamide (CTX) in mice. The mice were administered the PG–OJ extract or Shengmaiyin (SMY) at different proportions (1 : 0, 1 : 1, 1 : 2, 2 : 1, 2 : 3, 3 : 2, and 0 : 1). The changes in the chemical composition caused by decocting the herbs together were analyzed by HPLC. The parameters i.e. the number of bone marrow nucleated cells and peripheral blood cells and the thymus and spleen indices were determined after administration. The results indicated that the co-decoction of PG and OJ, especially at the ratio of 2 : 3, was more conducive to the conversion of conventional ginsenosides (Rg1, Re, Rb1, Rg2, Rc, Rb2, Rb3 and Rd) to rare ginsenosides (Rg5, Rk3, S-Rg3, R-Rg3, Rk1 and Rh1) and the dissolution of ophiopogonin D. In addition, PG–OJ has an excellent synergistic effect on myelosuppression induced by CTX in mice. PG–OJ could significantly increase the numbers of the bone marrow nucleated cells and peripheral blood cells; moreover, it increased the thymus index and decreased the spleen index. The herb pair with a ratio of 2 : 3 showed the best therapeutic effect. By combining the results of the chemical composition changes and pharmacological activities, it can be concluded that rare ginsenosides and ophiopogonin D may be the main material basis of PG–OJ for the treatment of bone marrow suppression after chemotherapy.