New medicines for treatment of osteoporotic bones have developed. In the previous studies, there were lots of pre-clinical experiments on animals to analyze the virtue of new medicine. However, the previous methods sacrificed a number of animals. They induced lots of expenses and ethical problems. In the present study, to investigate the effect of a medicine for osteoporosis by using in-vivo micro computed tomography (In-vivo Micro-CT, skyscan 1076, skyscan, Belgium) and micro finite element (*FE) analysis, morphological and mechanical characteristic changes of rat bone were detected and tracked. The 8 female Sprague-Dawley rats, used in the experiment, were randomized into 3 groups (Control, Sham and Risedronate group). The Risedronate (actonel, 0.58mg/Kg and 5days/week) for 8 weeks was administered in RIS group. The 4th lumbar vertebrae of rats were scanned by In-vivo Micro-CT with 35*m at week 0 (just before dose) and week 8 (after dose). Three-dimensional (3D) structural parameters were calculated. Simulated compression tests of 3D FE models were carried out to investigate the mechanical characteristics in the whole vertebral bone model of the 4th lumbar vertebra. The change rate of quantity and structure in Risedronate (RIS) group was smaller than that of control (CON) group. The change rate of structural modulus in RIS group was also smaller than that of CON group. This result shows the virtue of risedronate quantitatively as well as qualitatively. The study introduced the improved noninvasive biomechanical evaluation method, combined with In-vivo Micro-CT and *FE analysis, which was more effective and useful than the previous pre-clinical experiments.