Body fat accumulation and bone loss are both often associated with estrogen deficiency following menopause. In this study, we examined whether soy isoflavone, one of the phytoestrogens, and moderate exercise interventions exhibit cooperative effects on body composition and bone mass in ovariectomized (OVX) mice. Eight-week-old female mice were assigned to 6 groups: (1) sham-operated (sham); (2) OVX; (3) OVX with received a soy isoflavone diet (OVX+ISO); (4) OVX with exercised on a treadmill (OVX+EX); (5) OVX with given both isoflavone and exercise (OVX+ISO&EX); and (6) OVX with treated with 17 beta-estradiol subcutaneously (OVX+E2). Body composition and bone mineral density (BMD) were estimated by dual-energy x-ray absorptiometry (DXA). After the 6-week intervention, whole body fat (%) in the OVX group showed significantly higher than that in the sham group. Intervention of exercise and isoflavone alone partially inhibited OVX-induced body fat gain, and the combined intervention as well as E2 treatment completely restored fat mass to the sham level. Lean body mass in the whole body was not different in OVX group compared with that in OVX+ISO, OVX+EX, and OVX+E2 groups, but it was significantly higher in OVX+ISO&EX than in other groups. BMD of the whole body, lumbar spine, or femur showed significantly reduced by OVX, and the bone loss was partially inhibited by intervention of exercise or isoflavone alone. However, the combined intervention completely restored the bone mass to the level of sham, as did E2. Serum total cholesterol was significantly increased by OVX, which was normalized by the combined intervention or E2 treatment. These results demonstrate that combined intervention of soybean isoflavone and exercise prevented body fat accumulation in the whole body with an increase in lean body mass and restoration of bone mass, and reduced high serum cholesterol in OVX mice.