As is generally known, the lack of osteoinductive properties in titanium scaffolds has been a major barrier to bone defects repair. In our previous studies, we found that silicon-doped porous coatings prepared via micro-arc oxidation (MAO) had the potential application of Si-doped coatings in dental and orthopedic fields. We are currently focused on developing more advanced surface coatings to maximize their osteoinductive efficacy. Bone morphogenetic protein-2 (BMP-2), known for its ability to induce bone and cartilage development, has also been extensively studied. Therefore, in this study, macroporous titanium alloy scaffolds were fabricated using 3D printing technology, silicon ions were introduced onto the surface of customized macroporous titanium alloy scaffolds through MAO to enhance the bioactivity of the scaffolds, and BMP-2 was loaded onto the Si-doped coating to further improve the osseointegration of the titanium alloy scaffolds post-implantation. Results demonstrated that silicon-doped coating-loaded BMP2-modified multi-level porous titanium scaffolds exhibited improved hydrophilicity and biocompatibility. In-vivo and vitro studies further confirmed the superior bone regeneration capabilities of these scaffolds. This study demonstrates an optional strategy to combine two surface modification treatments, offering substantial potential as an advanced bone defect repair material with improved and accelerated bone regeneration.