Osteoporosis is a major problem in the elderly population worldwide. Low calcium intake and vitamin D blood level are risk factors for osteoporosis, and improving their intake is effective in patients with micronutrients deficiency. However, the effect of these interventions is ambiguous. Additive formula diet (AFD) contains fructo-oligosaccharide (FOS), isofiavone (ISO) and 1.0% citric acid Ca as a supplement for patients with osteoporosis. We aimed to investigate the effect of AFD on bone structure of the femur in ovariectomized rats. Sixteen 20-week old ovariectomized rats were randomly distributed into 2 groups; one group was fed normal diet (N, n = 8) and the second group was fed AFD (A, n = 8). Both groups were fed for 24 weeks, and body weight was measured at 8 and 24 weeks. After measuring the weight at 24 weeks, rats were euthanized using carbon dioxide. Lateral femur bone was extracted, and bone mineral density (BMD) and bone mineral content (BMC) were measured via micro computed tomography. Non-decalcified ground sections of the femur were examined via polarized-light microscopy. At 24 weeks, BMD and BMC were significantly higher for the A group than in the N group. The A group showed significantly better structural values with respect to Tb.Th, Tb.N, Tb.sp, Tb.spac and SMI than the N group. The A group showed significantly denser trabecular observations than the N group. Examination of the non-decalcified ground section from the A group showed strong polarized light properties of orange compared with sections from the N group. AFD may improve bone turnover in osteoporosis with the expectant decrease in the incidence of falls and bone fractures, which may enhance the quality of life of the elderly.