The perennial herb Saposhnikovia divaricata SCHISCHKIN, used as a source of traditional medicines, is known for its anti-bone erosion, anti-inflammatory, and analgesic effects. We examined the osteogenic properties of Sec-O-glucosylhamaudol (SOGH) extracted from S. divaricata roots as a bone-protective compound. We found that SOGH promoted osteoblast differentiation and mineralization and induced the expression of Bsp, Ocn, and Opn without any cytotoxic effects. SOGH also increased nuclear RUNX2 levels in pre-osteoblasts via the BMP2 and Wnt3a signaling pathways, but it had no evident effects on the autophagic and necroptotic signaling pathways. Furthermore, SOGH promoted bone-forming activities by inducing the adhesion and migration of osteoblasts and the expression of RUNX2 target proteins, including VEGF and MMP13. In sum, SOGH has osteogenic properties mediated via the BMP2 and Wnt3a signaling pathways and RUNX2 expression, indicating the bone-protective potential of this compound in diseases such as periodontitis and osteoporosis.