Single-factor delivery is the most common characteristic of bone tissue engineering techniques. However, bone regeneration is a complex process requiring multiple factors and specialized release mechanisms. Therefore, the development of a dual-delivery system allowing for programmed release kinetics would be highly desirable. Improvement of the molarity and versatility of the delivery system has rarely been studied. Herein, we report the development of a novel, modular programmed biphasic dual-release system (SCB), carrying a BMP2 and an engineered collagen I-derived recognition motif (Stath-DGEA), with a self-remodification feature on hydroxyapatite (HA)-based materials. The SCB system was loaded onto an additive manufactured (AM) scaffold in order to evaluate its bifactor osteogenic potential and its biphasic release behavior. Further, the biomechanical properties of the scaffold were studied by using the fluid-structure interaction (FSI) method. Section fluorescent labeling revealed that the HA scaffold has a relatively higher density and efficiency. Additionally, the results of the release and inhibition experiment suggested that the SCB system could facilitate the sustained release of therapeutic levels of two factors during the initial stage of implantation, thereby exhibiting a rapid high-dose release pattern at a specific time point during the second stage. The FSI prediction model indicated that the scaffold provides an excellent biomimetic mechanical and fluid dynamic microenvironment to promote osteogenesis. Our results indicated that incorporation of BMP2 with Stath-DGEA in the biphasic SCB system could have a synergetic effect in promoting the adhesion, proliferation, and differentiation of bone marrow mesenchymal stem cells (BMSCs) in vitro, under staged stimulations. Further, in vivo studies in both ectopic and orthotopic rat models showed that the SCB system loaded onto an AM scaffold could enhance osteointegration and osteoinduction throughout the osteogenic process. Thus, the novel synthetic SCB system described herein used on an AM scaffold provides a biomimetic extracellular environment that enhances bone regeneration and is a promising multifunctional, dual-release platform.