Abstract Scope In China, the root of M. officinalis has been widely used over thousands of years against a wide range of bone disease such as lumbago, limb-ache, sciatica and rheumatic arthralgia, and has tremendous medicinal value. But the bioactive constituents responsible for the osteoprotective effects in M. officinalis remain unknown. Methods and results M. officinalis polysaccharides were extracted, isolated and purified via DEAE-cellulose 52 and Sephacryl S-100HR column to obtain two saccharides (MOP70-1 and MOP70-2). The results of osteogenic activity assays revealed that MOP70-1 and MOP70-2 significantly promoted the proliferation, differentiation and mineralization of MC3T3-E1 cells. Furthermore, MOP70-2 also upregulated gene expression of runt-related transcription factor 2, osterix, osteocalcin, osteopontin, bone sialoprotein and osteoprotegerin, which implied that MOP70-2 stimulated osteoblastic differentiation by up-regulating osteogenic differentiation-related marker genes. In addition, structural analysis indicated that MOP70-2 contained (2 → 1)-linked- β -D-Fru f residues and terminated with a glucose residue. Morphological and conformational analyses indicated that MOP70-2 exhibited spherical structure of conglomeration and had no triple helix structure. Conclusion Our studies reported the osteogenic inulins obtained from root of M. officinalis for the first time. The systematical investigation including extraction, purification, biological activities and structural characterization provide a strong evidence for future therapeutic applications as anti-osteoporosis agent. Graphical abstract Unlabelled Image Highlights • Two polysaccharides (MOP70-1 and MOP70-2) were obtained from Morinda officinalis. • MOP70-2 exhibited more significant osteogenic activities than MOP70-1. • MOP70-2 stimulated osteoblast differentiation by up-regulating osteogenic genes. • The structure of inulin (MOP70-2) from M. officinalis was characterized. • MOP70-2 may act potentially as a natural anti-osteoporotic agent in future. [ABSTRACT FROM AUTHOR]