COX-2 specific inhibitor, which has been widely used, can delay bone fracture healing and reduce osteogenic potential of bone marrow stromal cells. However, it remains unknown how to prevent these side-effects of COX-2 inhibitor. In this study, we introduced BMP9-induced osteogenic differentiation as model to evaluate whether all-trans retinoic acid (ATRA) could ameliorate these adverse effects of COX-2 specific inhibitor on bone metabolism with in vitro and in vivo experiments, and uncover the possible mechanism underlying this process. Results showed that ATRA enhanced the potential of BMP9 to induce the osteogenic markers, such as alkaline phosphates (ALP) and mineralization; but retinoic acid receptor a (RARa) inhibitor showed the reversal effects. COX-2 specific inhibitor (NS398) reduced the osteogenic markers induced by BMP9, and ATRA almost eliminated the inhibitory effect of NS398. BMP9 up-regulated the protein level of β-catenin and promoted it translocate to nucleus, and both were reduced by NS398. On the contrary, ATRA notablely attenuated the inhibitory effect of NS398 on BMP9-increased β-catenin. Exogenous RXRa obviously ameliorated the inhibitory effect of silencing COX-2 on ectopic bone formation induced by BMP9. NS398 reduced the level of phosphorylated CREB, which was almost reversed by ATRA. Besides, RXRa interacted with phosphorylated CREB directly and both were recruited at β-catenin promoter region. Thus, we demonstrated that ATRA may reverse the side-effects of COX-2 inhibitor on bone metabolism through increasing the activation of Wnt/β-catenin pathway partly.