Accumulating evidence indicates that the interaction between immune and skeletal systems is vital in bone homeostasis. However, the detailed mechanisms between macrophage polarization and osteogenic differentiation of mesenchymal stromal cells (bone marrow-derived stromal cells [BMSCs]) remain largely unknown. We observed enhanced macrophage infiltration along with bone formation in vivo, which showed a transition from early-stage M1 phenotype to later stage M2 phenotype, cells at the transitional stage expressed both M1 and M2 markers that actively participated in osteogenesis, which was mimicked by stimulating macrophages with lower inflammatory stimulus (compared with typical M1). Using conditioned medium (CM) from M0, typical M1, low-inflammatory M1 (M1semi), and M2 macrophages, it was found that BMSCs treated with M1semi CM showed significantly induced migration, osteogenic differentiation, and mineralization, compared with others. Along with the induced osteogenesis, the autophagy level was the highest in M1semi CM-treated BMSCs, which was responsible for BMSC migration and osteogenic differentiation, as autophagy interruption significantly abolished this effect. This study indicated that low-inflammatory macrophages could activate autophagy in BMSCs to improve osteogenesis.