Objective To detect the cytokines in the bone marrow stromal cells (BMSCs) conditioned medium (neurobasal conditioned medium ,N-CM) that can regulate the differentiation of neural stem cells (NSCs) into high proportional neurons and explore the mechanism that BMSCs regulate the differentiation of NSCs.Methods The collected N-CM was divided into two parts(>5kD and <5kD)by means of ultrafiltration after misce bene. The two parts were used to culture NSCs separately, and the effective part that could regulate the differentiation of NSCs was detected by protein microarray analysis. Results The N-CM>5kD could promote the NSCs to differentiate into high proportional neurons, so this part was detected by protein microarray analysis, 7 cytokines CINC-3, CNTF, IFN-γ, IL-1α, MCP-1, TIMP-1and VEGF were detected to up-regulate 1.5 times compared with the neurobasal medium (molecular weight above 5kD). Conclusion The dissolvable molecules excreted by BMSCs could promote the NSCs to differentiate into neurons. Some cytokines with the molecular weight of above 5kD play a crucial role during this process.