The quantity and function of osteoblasts require continuous osteogenic differentiation of bone marrow mesenchymal stem cells. Recent evidence suggests that microRNAs (miRNAs) act as important post-transcriptional regulators in a wide range of biological processes, including osteoblastic differentiation. Quercetin has also been found to prevent bone loss. In this study, we investigated the osteogenesis of quercetin and miR-206 on bone marrow mesenchymal stem cells (BMSCs) and their relationship. We observed quercetin enhanced BMSCs proliferation with a dose-dependent manner in Cell Counting Kit-8 (CCK-8). Alizarin red S staining, alkaline phosphatase (ALP) quantification assay, miR-206 and mRNA levels of osteogenesis marker genes by quantitative real-time PCR (qPCR) were used to analyze osteogenic potential. We observed quercetin significantly elevated bone mineralization and the mRNA expression levels of osteoblast-specific genes including Runt-related transcription factor 2 (Runx2), Osterix (OSX), osteocalcin (OCN), and osteopontin (OPN). Correspondly, Cx43 expression were increased, while miR-206 expression were decreased. In the presence of agomir of miR-206, effects of quercetin on mineralization, alkaline phosphatase activity and osteoblast-specific genes expression were suppressed. Most of all, Cx43 protein level was also blocked while overexpression of miR-206 against quercetin effects. Taken together, these data indicated that quercetin promotes BMSCs proliferation and osteogenic differentiation. The osteogenic effect of quercetin is partly modulated through miR-206/Cx43 pathway.