In this study, the in vivo and in vitro osteogenesis was successfully induced in situ by the controlled release of alendronate (AL) and dexamethasone (Dex) from the poly(lactic-co-glycolic acid) (PLGA)/hydroxyapatite (HA) sintering microsphere scaffold (SMS). This microspherically based controlled release system is constructed with two-levels of structure: AL attached HA particles and a Dex-PLGA matrix. Bone marrow mesenchymal stem cells (BMSCs) cultured on AL loaded PLGA/HA sintering microsphere scaffold (PLGA/HA-AL-SMS) and AL-Dex loaded PLGA/HA sintering microsphere scaffold (PLGA/HA-Com-SMS) displayed a strong osteogenic commitment locally in vitro. The osteogenic commitment of BMSCs on the scaffolds were verified by an alkaline phosphatase (ALP) activity assay, real time-PCR and immunohistochemistry analysis. The results demonstrated that BMSCs cultured on PLGA/HA-AL-SMS and PLGA/HA-Com-SMS exhibited superior osteogenic differentiation owing to significantly high gene expression of typical osteogenic genes–osteocalcin (OC), type I collagen, BMP-2, and also protein secretion of type I collagen. In addition, BMSCs laden with PLGA/HA-AL-SMS and PLGA/HA-Com-SMS were also implanted into the back subcutis of mice and bone defects surgically created on rabbit femurs. The histology and immunohistochemistry results indicated that the scaffolds promoted BMSCs osteogenic commitment and also the new bone formation in vivo. In conclusion, this controlled release system is promising for implanted biomedical devices to improve bone reparation and regeneration.