Objective To explore the effects of bone marrow mesenchymal stem cells (BMSCs) transplantation or parathyroid hormone (PTH) alone or combined together on related indices of bone density in osteoporotic rats. Methods Fifty female SD rats were divided into groups A, B, C, D and E, 10 animals in each group. Bilateral ovaries were removed in the rats from groups B, C, D and E, while for those from group A, adipose tissue around the ovaries was only removed. In 12 weeks after operation, 3 rats were selected from each group, and then the estrogen level and bone density related indices such as trabecular number (Tb.N), trabecular thickness (Tb.Th), trabecular separation (Tb.Sp) and bone volume to tissue volume (BV/TV) were measured. SD healthy male rats were sacrificed to isolate and culture BMSCs, and the obtained cells were further identified with single labeling flow cytometry. At 12 weeks after operation, except those from groups A and B getting no intervention, subcutaneous injection of 60 μg/kg rat PTH 1-34 on the back (once every other day, for 12 consecutive weeks) was given to group C and the injection of 5×10⁸/ml BMSCs on the bilateral femoral neck were given to the group D, and group E were given the same intervention as group C on the basis of group D. The rest 7 rats in five groups were sacrificed in 12 weeks after intervention. Tb.N, Tb.Th, Tb.Sp and BV/TV of femoral neck were measured by micro-CT scanning. SPSS statistics 20.0 was used for statistical analysis. One-way ANOVA was employed for comparisonamong groups, and LSD test was applied for those with statistical significance. Results Compared with group A, the estrogen level, Tb.N, Tb.Th and BV/TV in groups B, C, D and E were decreased significantly, and Tb.Sp was increased significantly (P<0.05), but there was no significant differences among groups B, C, D and E (P>0.05), and the rats in group B, C, D and E were identified as osteoporotic rats. Single-labeling flow cytometry showed that CD29 (99.86%) and CD90 (99.73%) were expressed in the third passaged (P3) BMSCs, while CD34 (6.48%) and CD45 (0.94%) were rarely expressed, which proved that BMSCs were successfully cultured. After 12 weeks of intervention, micro-CT scanning showed that PTH or BMSCs alone, or combination improved bone microstructure, but they did not reach the level of group A. Compared with group B, Tb.N, Tb.Th and BV/TV in groups C, D and E were increased significantly, while Tb.Sp was decreased significantly (P<0.05). Compared with groups C or D, Tb.N, Tb.Th and BV/TV in group E were increased significantly and Tb.Sp was decreased significantly (P<0.05). Conclusion The effect of BMSCs combined with PTH in the treatment of local osteoporosis is better than that of single use.