The ability to regulate the spatial distribution of nanoparticles to generate patterns/arrays makes them promising applications in various fields. Here, a versatile and potential method, based on the polymer brushes patterned surface with hydrophilic-hydrophobic contrast characteristic, was developed to create the nanoparticle patterns with complicated architectures and controllable structural colors on the silicon/glass substrate. Employing DMD-mediated Photo-ATRP process, the selective growth of hydrophilic poly (ethylene glycol) methyl acrylate (PEGMA) brushes on the surface functionalized with hydrophobic initiators was achieved. Subsequently, the as-obtained hydrophilic-hydrophobic patterned substrate was acted as a template for regulating the assembly behavior and spatial arrangement of polystyrene (PS) nanoparticles, leading to the generation of nanoparticle patterns with desired architectures. Especially, the assembly densities could be controlled via tuning the grafting density of patterned PEGMA brushes, which enabled the effective regulation of structural color on the patterned surface. On the basis of the spatiotemporal control of patterned hydrophilic region formation, the sequential assembly of different nanoparticles on the same substrate could be achieved, allowing for a multi-component nanoparticle pattern for structural color-based anticounterfeiting application. The presented technique for the creation of nanoparticle patterns/arrays exhibits a tremendous practical potential in various fields including high-throughput preparation of structural colors, anticounterfeiting/ information encryption, and optical hypersurfaces.