Structural DNA Nanotechnology facilitates the precise and versatile fabrication of nanomaterials possessing complex geometries and functionalities. DNA-silica composites (DSCs), as representative hybrid materials, demonstrate distinctive application potential in emerging fields such as nanophotonics and nanoelectronics. However, achieving precise control over the silica shell thickness remains a significant challenge in silicification processes utilizing DNA nanostructure templates. This study investigates the effect of organoalkoxysilanes (OASs), varying in substituent type and quantity, on DNA-templated silicification. We identify a negative correlation between the number of substituents on the OAS precursor and the resulting silica shell thickness, enabling nanometer-scale control. Compared to conventional tetraethyl orthosilicate (TEOS), the tailored OAS variants significantly reduce silica shell thickness while simultaneously enhancing DSC monodispersity, achieving values up to 76.7% following 24-h reactions. Furthermore, a positive correlation is established between the substituent steric occupancy ratios and the monodispersities of DSCs. Our approach also enables effective diversification of the surface functionalities of DSCs. These advances provide critical foundational support for the application of DSCs in nanofabrication, photonic crystal engineering, and interdisciplinary domains.