In this work, we designed a two-step method to prepare carbon-incorporated silica from rice husk biomass. This two-step method could promote the chemical bonding between carbon and silica that is responsible for the generation of photoluminescence and effectively remove free carbon in the final product that is responsible for the quenching of photoluminescence. Such a structural optimization of the carbon-incorporated silica derived from rice husks led to a significant improvement in its photoluminescence with the emission band covering the entire visible spectrum. The toxicity of the carbon-incorporated silica from rice husks was 2-fold lower compared to commercial crystalline and amorphous spherical silica. Therefore, such rice husk-derived carbon-incorporated silica by the two-step method is promising for widespread application.