Abstract: OBJECTIVE To compare the potential genes and pathways involved in the preventive treatment of ovariectomized (OVX)-induced osteoporosis in bone marrow mesenchymal stem cells (BMSCs) obtained from OVX rats treated with Zuogui Pill and Estradiol valerate. METHODS A total of 36 rats were divided into four groups: Model， Sham (Control)， Zuogui Pill， and Estradiol valerate. The rats in the last two groups were intragastrically administered with Zuogui Pill or Estradiol valerate， respectively， from 2 weeks post operation to 4， 8， and 12 weeks post operation. The rats in the other two groups were treated with distilled water. The gene expression patterns in BMSCs were investigated， which were subjected to bioinformatics analyses， including identification of differentially expressed genes (DEGs)， pathway enrichment and correlation analyses， weighted correlation network analysis (WGCNA)， and protein-protein interaction (PPI) network construction. RESULTS At 12 weeks post operation， bone mineral density in OVX model group significantly decreased. Meanwhile， bone mineral densities in Zuogui Pill and Estradiol valerate groups were significantly higher than that in the model group， indicating that the models were constructed successfully， and both traditional Chinese medicine and western treatment could improve the bone density of OVX rats. Numerous DEGs were identified in different groups at different time points. Difference analysis showed that compared with the model group， 405， 403 and 618 DEGs were screened in Zuogui Pill treatment group at 4， 8 and 12 weeks after surgery， respectively， and 78， 326 and 232 DEGs in Estradiol valerate group. Pathway analysis showed that these DEGs were closely related to inflammation- and immunity-associated pathways， such as herpes simplex infection (Il1b and Tnf)， the PI3K-Akt signaling pathway (Itga2 and Fgf21)， and leukocyte transendothelial migration (Cxcl12). WGCNA identified several key modules that were significantly linked to the PI3K-Akt signaling pathway and inflammatory bowel disease. The PPI network in the Zuogui Pill group included 388 nodes and 133 nodes in the Estradiol valerate group. CONCLUSION The results of this study suggest the importance of inflammation and immunity in the pathogenesis of OVX-induced osteoporosis in bone marrow microenvironment. The identified pathways and genes may serve as therapeutic targets for this disease.