Demands for natural products, in the form of botanicals, dietary supplements, and herbal medicine, for management of chronic diseases are increasing globally. Natural products might be an alternative for the management of bone health to meet the demands of a growing aging population. Different types of natural products, including Chinese herbal medicine decoctions, herbs, and isolated phytochemicals, have been demonstrated to exert bone protective effects. The most common types of bone protective bioactives are flavonoids, stilbene, triterpenoids, coumestans, lignans, and phenolic acid. The actions of natural products can be mediated by acting systemically on the hormonal axis or locally via their direct or indirect effects on osteogenesis, osteoclastogenesis, as well as adipogenesis. Furthermore, with the use of metabolomic and microbiome approaches to understand the actions of natural products, novel mechanisms that involve gut-brain-bone axis are also revealed. These studies provide evidence to support the use of natural products as bone therapeutics as well as identify new biological targets for novel drug development.