To understand the material basis and underlying molecular machinery of antiosteoporosis activity of the Flos Chrysanthemi Indici (FCI), the consequences of ethanol extract on the bone loss in mice induced due to ovariectomy (OVX) was evaluated. Also, the antiosteoporosis fraction obtained from the FCI ethanol extract was isolated and purified using a preparative high-speed countercurrent chromatography (HSCCC). The in vitro impact of the compounds was investigated on osteoblast proliferation and differentiation. The results revealed that ethyl acetate fraction with robust in vivo antiosteoporosis activity was obtained. The important compounds purified by HSCCC using gradient elution system included acacetin, apigenin, luteolin, and linarin. The four compounds enhanced the differentiation and proliferation of osteoblasts in MC3T3-E1 cells. They also augmented the mRNA levels of runt-related transcription factor 2 (Runx2), osteocalcin (OCN), osteopontin (OPN), and type I collagen (COL I). The AKT signaling pathway was also activated in MC3T3-E1 cells by the four compounds. The present study demonstrated that the antiosteoporosis effects of FCI did not depend on a single component, and HSCCC efficiently isolated and purified the antiosteoporosis bioactive compounds from FCI.