Spatiotemporal control of exogenous growth factors plays a crucial role in the sequential repair of damaged tissues. However, traditional therapeutic trials have mostly relied on the delivery of a single molecule because of the limitations of rapid diffusion and the instability of biomolecules. In this study, we developed a novel strategy using a composite of gelatin and silica as an alternative for the stable and sequential release of biomolecules. Two biomolecules, basic fibroblast growth factor and bone morphogenetic protein-2, were incorporated into two separate composites and sequentially layered onto the activated polymer surface. Each molecule was sequentially released from each layer of the scaffold and the silica composite prevented rapid diffusion owing to its nano-porous structure. The adhesion, proliferation, and osteogenic differentiation of rat bone marrow-derived mesenchymal stem cells were significantly enhanced in the double-layered group containing separately delivered dual molecules compared with the control or single groups. Our developed gelatin–silica composite was successfully placed in double layers on polymer scaffolds, and cellular responses were promoted in this manner. These results demonstrated that our scaffolding system has potential as a therapeutic strategy for the delivery of dual or multiple biomolecules in regenerative medicine.