Rheumatoid arthritis, osteoarthritis, and periodontal disease are bone destructive diseases mainly caused by inflammation. Various studies are being conducted to develop treatments for inflammatory bone destructive diseases. Many of these studies involve plant-derived natural compounds. In these studies, cell differentiation, signal transduction pathways, and bone resorption were measured at the cellular level. In disease-induced animal models, the amount of inflammatory mediators or matrix destructive enzymes and serum metabolic markers were measured. This study examined the effects of plant-derived natural compounds, such as flavonoids, on inflammatory bone destructive diseases. In addition, we structurally classified various substances used to maintain bone health and summarized the biological effects and related mechanisms of the components.