To evaluate the mechanical contributions of the spongiosa and cortex to the whole rat vertebra, we developed a finite element analysis (FEA) system linked to three-dimensional data from microcomputed tomography (micro-CT). Twenty-eight fifth lumbar vertebrae (L-5) were obtained from 10-month-old female rats, comprised of ovariectomized (ovx, n = 6), sham operated (n = 7), and alfacalcidol-treated after ovx (0.1 μg/kg [n = 8] and 0.2 μg/kg [n = 7]) groups. The trabecular microstructure of L-5 was measured by micro-CT. Yield strength at the tissue level (YS), defined as the value at which 0.034% of all elements reached yield stress, was calculated by the FEA. Then, the ultimate compressive load of each specimen was measured by mechanical testing. The YS of the whole bone (YSw) showed a significant correlation with ultimate load (r = 0.91, p < 0.0001). The YS values of the isolated spongiosa (YSs) and cortex (YSc) were calculated in models with varying amounts of trabecular or cortical bone mass. The mechanical contribution of the spongiosa showed a nonlinear relationship with bone mass, and ovx reduced the mean mechanical contribution of the spongiosa to the whole bone by 13% in comparison to the sham group. YSs had a strong relationship with trabecular microstructure, especially with trabecular bone pattern factor (TBPf) and structure model index (SMI), and YSc had a strong relationship with cortical bone volume. The structural parameters most strongly related to YSw were BV/TV and TBPf. Our micro-FEA system was validated to assess the mechanical properties of bone, including the individual properties of the spongiosa and cortex, in the osteoporotic rat model. We found that the mechanical property of each component had a significant relationship with the respective bone mass, volume, or structure. Although trabecular microstructure has a significant relationship with bone strength, in ovx bone with deteriorated trabecular microstructure, the strength depended mainly on the cortical component.