We have reported that genistein (Gen) and silicon (Si) have synergistic effects on ovariectomy-induced bone loss in rat; however, the potential mechanisms behind this effect were not fully clarified yet. This study was performed to evaluate the bone protective mechanisms of concomitant intake of genistein and silicon in ovariectomized rat by OPG/RANKL axis. Three-month-old Sprague-Dawley female rats were subjected to ovariectomy (OVX) or sham surgery; after surgery, the OVX rats were randomly divided into five groups: OVX-Gen, OVX-Si, OVX-Gen-Si, OVX-E, and OVX. Genistein, silicon, and 17β-estradiol supplementation were started after ovariectomy and continued for 10weeks. The results showed that genistein and silicon treatment increased the bone mineral density (BMD) of ovariectomized rats. In addition, the BMD of the tibia and femur were highest in the OVX-Gen-Si group compared with OVX-Gen and OVX-Si group (p < 0.05). After 10weeks treatment with genistein and silicon, the bone structure of ovariectomized rats was recovered, there was no difference of bone histomorphometric parameters between OVX-Gen-Si, OVX-E, and SHAM group (p > 0.05), and there was no difference in the concentration of serum ALP, Ca, P, OPG, and RANKL between OVX-Gen-Si, SHAM, and OVX-E groups (p > 0.05). RT-PCR showed that genistein and silicon treatment could effectively increase the OPG mRNA expression and decreased the RANKL mRNA expression compared to that of the OVX group (p < 0.05), the OPG/RANKL mRNA ratios were significantly decreased in the OVX group (p < 0.05), and it was nearly to normal in the OVX-Gen-Si group. Immunohistochemical staining results showed that genistein and silicon supplementation could effectively increase the protein expression of OPG and decrease the protein expression of RANKL in bone tissues; there were no significant differences in OPG and RANKL positive expression areas between OVX-Gen-Si, SHAM, and OVX-E group (p > 0.05). The results above indicate that genistein and silicon supplementation can effectively reduce RANKL, increase OPG levels, and OPG/RANKL ratios in the serum and bone tissue of ovariectomized rats; this is the main mechanism by which genistein and silicon play a bone protective role in ovariectomized rats.