A method for preventing or treating a bone disease, includes administering to a patient having the bone disease a pharmaceutical composition comprising glyceollin as an active ingredient. The active ingredient, glyceollin promotes degradation of the Runx2 protein in osteoblasts and inhibits the mRNA expression of Rankl in osteoblasts to prevent the differentiation of osteoclasts. Furthermore, glyceollin is capable of ameliorating osteoporosis in animal models for osteoporosis. The composition promises drug or food for prevention or treatment of not only osteoporosis but also bone diseases caused by cancer metastatic to the bone.