The compatible carbon-silicon complex materials originated from precursor diglycerylsilane (DGS) and sugar-modified silane N-(3-triethoxysilylpropyl)gluconamide (GLS) have gained substantial popularity by demonstrating admirable properties to stabilize entrapped biomolecules. The microenvironment inside these materials, especially the distribution of sugar moieties inside the matrix, which is likely the most critical factor determining compatibility of these materials, still remains unclear. To deeply investigate the biocompatibility mechanism of these materials, we have adopted two different preparation routes for these materials by introducing GLS into the starting DGS sol stage, but things are different after the DGS gel is formed. A fluorescence probe rhodamine 6G is introduced herein in the DGS sol to monitor the distribution of GLS moieties, as well as the evolution of the microenvironment inside resulting materials. All in all, the findings demonstrated that the timing of GLS addition plays a critical role in controlling the evolution of the inner structure of materials, suggesting that this factor provides a promising route to tune the properties of the resulting materials.biocompatibility, carbon-silicon complex, microenvironment, characterization