A novel bi-isoflavonoid, podocarnone (1), together with five known flavonoids, namely genistein (2), afzelin (3), astragalin (4), luteolin (5) and pratensein (6), were isolated from the whole plants of Podocarpium podocarpum (DC.) Yang and Huang for the first time. The structure of podocarnone (1) was elucidated by detailed spectroscopic analyses, including 1D and 2D NMR techniques. All the isolated compounds were evaluated for their proliferative effects on osteoblasts derived from neonatal rat calvaria and inhibitory effects on multinucleated osteoclasts from rat marrow cells so as to explore the antiosteoporotic activity of these components. Podocarnone (1) exhibited potent stimulatory effects on osteoblastic proliferation and ALP (alkaline phosphatase) activity, and significantly inhibited the activity of osteoclastic TRAP (tartrate-resistant acid phosphatase) in the low concentration range of 10−12–10−14 mol/L, which were equivalent to the activity of genistein (2) in the concentration range of 10−7–10−9 mol/L. The other five known flavonoids also showed varied degrees of antiosteoporotic activities, and structure–activity relationship analysis revealed the number of phenolic rings contained in these structures maybe responsible for the antiosteoporosis property.