Objective: To compare the decrease of bone mineral density (BMD) in osteoporosis model. Analyze the difference of lncRNA in cultured bone marrow mesenchymal stem cells (BMSC) in osteoporotic model rats and the functions of the difference lncRNA. Methods: 12 SD rats were equally divided into osteoporosis model group and control group. The osteoporosis model was made by ovariectomized. BMD in ovariectomized SD rats in osteoporosis group and in control group were determined by dual-energy X-ray bone mineral density detector, and were compared with each other. BMSC from SD rats femur bone marrow were cultured in vitro. Detect the difference expression of lncRNA in BMSCs of osteoporosis model(n=3) and control group(n=3) by gene chip technology, and the different biological functions and related signaling pathway analysis of lncRNA were analysed by GO function analysis and the KEGG enrichment. Results: BMD in osteoporosis model SD rats after 3 months was （157.33±6.28）mg/cm2,decreased significantly compared with control group rats（183.33±4.50）mg/cm2（P<0.05）. A total of 32759 gene fragments were detected in BMSCs in the osteoporosis model group and the control group, and 8454 lncRNA gene fragments had significant difference（P<0.05）, among which 3593 were up-regulated and 4861 were down-regulated in osteoporosis model group. 4992 lncRNA gene fragments were detected. According to |log2FC|>1 and P<0.05 evaluation standard, 116 lncRNA gene fragments in BMSCs of osteoporosis model rats were significant differences, which 35 raised and 81 declined. Differential lncRNAs are mainly involved in the biological process of cell growth and development, and mainly regulate protein transport pathways. Conclusion: Removal of ovaries can reduce BMD in SD rats. There were differences in the expression of lncRNA in BMSC in osteoporosis model rats and normal rats, and the differentially expressed lncRNA involved in the regulation of BMSC growth and development process and protein transport pathway.