Objective: To evaluate the protein expression and distribution of Notch signaling-related, differentially expressed genes (DEGs) in the bone marrow cells of S180 tumor bearing mice. Additionally, verification of acupuncture regulated protein expression of these DEGs to protect bone marrow stem cells and alleviate cyclophosphamide (CTX) chemotherapy-induced myelosuppression was examined as well. Methods: Healthy male Kunming mice were inoculated with S180 sarcomas and further divided into blank control (group A), CTX group (group B), acupuncture (group C), and moxibustion (group D) groups. Animals in groups B, C, and D were intraperitoneally injected with single dose of 150 mg/kg CTX to generate the myelosuppressive model; while animals in group A were injected with an equivalent volume of sterile saline. After immobilizing the animals, mice in groups C and D received daily acupuncture and moxibustion, respectively at Dazhui, Geshu, Shenshu, and Zusanli acupoints; while mice in groups A and B received no daily treatment. Animals in each group were euthanized by cervical dislocation following five days of treatment and their femurs collected for marrow harvest. Small-throughput cDNA microarray was used for initial DEG screening, followed by immunohistochemistry, real-time quantitative PCR (RT-qPCR), and Western Blot analysis to detect protein expression and quantity of the Notch signaling-related DEGs in the bone marrow cells. Results: Expression of numb proteins (i.e., numb1 and numb2) was found to be up regulated while notch2 and jag1 were down regulated in bone marrow cells of acupuncture treated, tumor bearing mice. Conclusion: Acupuncture regulated the changes of Notch signaling-related DEGs in mouse bone marrow cells. The data indicates that acupuncture treatment may alleviate the CTX chemotherapy-induced myelosuppression associated with tumor burden, suggesting that might be the key mechanism to improve bone marrow function.