Background: The differentiation of bone marrow mesenchymal stem cells (BMSCs) is a complex and dynamic process. The gene expression pattern and mechanism of different periods of adipogenic and osteogenic differentiation remain unclear. Additionally the inaction between these two lineages determination requires further exploration. Results: Five modules that are most significantly associated with osteogenic or adipogenic differentiation of BMSCs were selected for further investigation. Biological terms, such as ribosome biogenesis, TNF-α signaling pathway, glucose import, fatty acid metabolism along with hub transcript factors, such as PPARG, YY1, and hub miRNAs, such as hsa-mir-26b-5p were enriched in different modules. The expression pattern of 6 hub genes, ADIPOQ, FABP4, SLC7A5, SELPLG, BIRC3, and KLHL30 were validated by RT-qPCR. In the end, cell staining experiments extended the findings of bioinformatics analysis.Conclusion: This study identified the key genes, biological functions, and regulators of each time point of adipogenic and osteogenic differentiation of BMSCs and provided novel evidence and ideas for further research on the differentiation of BMSCs.