The diblock copolymer polystyrene-block-polyethylene oxide forms phase-separated cylindrical nanopatterns with two oriented phases perpendicular to the substrates, which provides a great opportunity for directed flow/diffusion through one of the phases. This work aims to construct a nanopattern of nanoparticles on a surface using the directed diffusion of metal nanocrystals through hydrophilic polyethylene oxide (PEO) domains onto the surface, where specific bonding interactions between the nanocrystals and the surface chemical functionality occurs to immobilize the gold nanoparticles on the surface. Gold nanocrystals approximately 12 ± 3 nm in size are allowed to diffuse through about 21 ± 1 nm swollen PEO domains on aminopropyltrimethoxysilane-modified silicon and react with the amino groups via chelating or ion-pairing interactions, forming uniform Au nanodot patterns. The Au nanodot patterns can be used for further attachment, for example, grafting polymer brushes. The morphology of the Au nanopatterns evolves with polymer growth until the Au nanodots are completely masked by polymer brushes. The Au nanopatterns can also be used as substrates for microcontact printing initiators followed by polymer grafting, i.e., nanolithography (20–30 nm, block copolymer) and micropattern technology (2–20 μm, PDMS stamps), which are combined in this manner to construct a dual-patterned structure.