Liquid phase deposition (LPD) is a useful method for the production of oxide film with low reaction temperature and production cost. With the report that the LPD of oxide films is conformally processed with uniform thickness and composition, there has been significant attention given to investigating its kinetic controls and growth mechanism on the flat surface. In this work, we explored the LPD of silicon dioxide on the hexagonally close-packed silica beads array as a nanostructured surface. The deposition and etching reactions of SiO2 occurred locally and simultaneously on silica beads, and were distinguished from the amount of fumed silica added in LPD solution. From locally competitive reactions, we obtained the anisotropic morphology of close-packed silica beads, and proposed a mechanism for the local LPD of SiO2 driven by nanostructured surfaces. This work contributes highly to improve metal oxide-based engineering, and also provide greater insight into the topography-driven LPD.