In this work, carbon quantum dot grafted silica nanoparticles (silica–C NPs) are directly synthesized from rice husk biomass with high yield. The rice husk derived silica–C NPs exhibit outstanding features, including ease of surface modification, high water dispersibility, and biocompatibility. Due to the covalent decoration of the carbon framework, the wide band gap amorphous silica is endowed intense and unique photoluminescence, which can be well controlled by further adjustments. Detailed investigations suggest that the silica–C NPs have the inherent advantages of both silica and carbon quantum dots, which ideally addresses the widely recognized issues of conventional silica-based photoluminescent nanomaterials for biomedical applications. In addition to creating a novel silica-based nanostructure with prominent performances, this work achieves the comprehensive utilization of rice husk biomass, which shows significant economic and environmental benefits.