Poly(ε-caprolactone) (PCL) has received considerable attention in bone tissue engineering. However, the lack of osteoinductive ability of PCL limits its application. The aim of this study was to directly attach bone morphogenetic protein-2 (BMP-2) to PCL scaffolds by a crosslinking conjugation method and to investigate whether the bound BMP-2 maintained bioactivity in vitro. Immunofluorescent staining against BMP-2 and quantitative enzyme-linked immunosorbent assay measurements demonstrated that BMP-2 was successfully immobilized on the PCL three-dimensional scaffold by aminolysis and subsequent chemical conjugation. Conjugation produced much higher immobilization efficiency than the physical adsorption. Conjugated BMP-2 release from the PCL scaffolds was significantly slower than that from BMP-2-adsorbed PCL scaffolds over 15 days, which resulted in more BMP-2 locally retained on the conjugated scaffold. Further, the downstream Smads pathway was upregulated in bone marrow stromal cells cultured on the BMP-2-conjugated PCL scaffolds. Finally, gene expression of osteogenic markers (alkaline phosphatase, osteoclacin, and type I collagen) was upregulated in bone marrow stromal cells cultured on the PCL scaffolds with BMP-2 conjugation, but not on PCL scaffolds after BMP-2 adsorption. Therefore, our finding demonstrated that BMP-2 conjugation on polyester scaffolds is a feasible way to impart scaffolds with osteoinductive capability.