The present invention relates to a method and a system for selecting an osteoporosis therapeutic agent based on protein damage information of an individual by using individual genome sequencing. The method and the system, according to the present invention, are highly reliable and widely applicable techniques capable of predicting side effects or risks of specific drugs, in other words, osteoporosis therapeutic agents, for each individual by performing sequence analysis of an exon part of a gene that codes various proteins involved in pharmacokinetics or pharmacodynamics of osteoporosis therapeutic agents.