In this study, the change of the natural frequencies in mouse femurs with osteoporosis was investigated based on a vibration test and a finite element. Three groups of the femurs include the osteoporotic group, the treated group and the normal group. In the vibration test, the natural frequencies were measured by the mobility test. For the finite element analysis, the micro finite element model of the femur was reconstructed using the Micro-CT images and the Voxel mesh generation algorithm. From the results, the averaged natural frequencies in the osteoporotic group were the highest, followed by those in the treated group. The finite element models were validated within 15% errors by comparing the natural frequencies in the finite element analysis with those in the vibration test. The developed Micro-CT system, the Voxel mesh generation algorithm, the presented finite element analysis, and vibration test could be useful for the investigation of the structural change of the bone tissue, and the diagnosis and the treatment in the osteoporosis.