DNA origami has been widely investigated as a template for the organization of various functional elements, leading to potential applications in many fields such as biosensing, nanoelectronics, and nanophotonics. However, the synthesis of inorganic nonmetallic nanomaterials with predesigned patterns using DNA origami templates has seldom been explored. Here, a novel method is reported to site-specifically synthesize silica nanostructures with designed patterns on DNA origami templates. The molecular dynamic simulation confirms that the positively charged silica precursors have a stronger electrostatic affinity to protruding double-stranded DNA (dsDNA) than DNA origami surfaces. The work describes a novel strategy to fabricate silica nanostructures with nanoscale precision. Moreover, the site-specific silicification of DNA nanoarchitectures expands the scope of customized synthesis of inorganic nonmetallic nanomaterials.