[Objective] To evaluate the characteristics of vertebrae and long bone in early stage after ovariectomy in female rats by micro CT imaging and biomechanical test based on histomorphology. [Methods] Fifty 12 weeks old female rats were randomly divided into two groups (n=25). Control group was given sham operation, and ovariectomized group was given ovariectomy. Five rats in each group were randomly selected at 1 week, 4 weeks, 8 weeks, 12 weeks and 16 weeks after operation.[Results]The bone mass and trabecular microstructure of lumbar vertebrae and femur measured by micro CT decreased at 4 weeks after ovariectomy, and the difference was statistically significant (P＜0.05). The biomechanical properties of vertebral body had no significant difference at each time point (P＞0.05), but the biomechanical properties of femur had significant difference only at 1 week after ovariectomy (P＜0.05).[Conclusion]Our experimental results show that the bone strength of vertebral body and femur does not change significantly in the early stage, and the bone loss patterns of vertebral body and long bone are not the same. Micro-CT can timely and accurately reflect the changes of bone trabecular microstructure in the early stage of postmenopausal osteoporosis, and provide certain technical support and theoretical guidance for early clinical screening and bone health protection.