Alpha-tricalcium phosphate (α-TCP) based porous scaffolds have superior osteoconduction and osteoinduction in bone tissue engineering, furthermore, these 3D porous scaffolds can be used as efficient drug delivery carriers. In the concept of tissue engineering, the “drugs” could be defined as drug molecules or biomacromolecules, even cells. These “drugs” have endowed the scaffolds which were laden improved abilities compared with the blank scaffolds. In this study, we anchored osteogenic bone morphogenetic protein-2 (BMP-2) derived peptides to α-TCP 3D porous scaffolds by linking the E7 domain to the target peptides, constructed the modified active peptides (E7BMP-2 peptides) delivery system, which finally achieved the modified peptides sustaining release and enhanced rat bone marrow mesenchymal stem cells (BMSCs) osteogenic differentiation in vitro. The α-TCP 3D porous scaffolds had micropores and interconnected micropores which expanded surface area of the scaffolds. The release test testified the constructed the delivery system had realized long-term release in which the peptides dosage could be detected by the BCA protein assay kit after 10 days compared with BMP-2 proteins which absorbed on the same α-TCP 3D porous scaffolds. The constructed E7BMP-2 peptides delivery system supported rat BMSCs osteogenic differentiation in the form of improving the genes expression levels of Runx2, ALP and OCN. Based on electrostatic interactions, E7 domain fastened combination between the active BMP-2 derived peptides and the α-TCP 3D porous scaffolds, the sustaining E7BMP-2 peptides release promoted the BMSCs osteogenesis as BMP-2 proteins did, which endowed α-TCP 3D porous scaffolds enhanced osteoinductive abilities in vitro.