Bone fractures and defects pose serious health-related issues on patients. For clinical therapeutics, synthetic scaffolds have been actively explored to promote critical-sized bone regeneration, and electrical stimulations are recognized as an effective auxiliary to facilitate the process. Here, we develop a three-dimensional (3D) biomimetic scaffold integrated with thin-film silicon (Si)-based microstructures. This Si-based hybrid scaffold not only provides a 3D hierarchical structure for guiding cell growth but also regulates cell behaviors via photo-induced electrical signals. Remotely controlled by infrared illumination, these Si structures electrically modulate membrane potentials and intracellular calcium dynamics of stem cells and potentiate cell proliferation and differentiation. In a rodent model, the Si-integrated scaffold demonstrates improved osteogenesis under optical stimulations. Such a wirelessly powered optoelectronic scaffold eliminates tethered electrical implants and fully degrades in a biological environment. The Si-based 3D scaffold combines topographical and optoelectronic stimuli for effective biological modulations, offering broad potential for biomedicine.