With well-established surface-chemical properties, monodisperse silica-coated Au nanoparticles (Au@SiO2) were first functionalized with the silane reagent 3-gylcidoxypropyltrimethoxysilane (GPTS). Then, these epoxy-terminated Au@SiO2 nanoparticles could be easily assembled onto the silicon surface, which has been patterned with 3-aminopropyltriethoxysilane (APS) SAMs and octadecyltrichlorosilane (OTS) SAMs alternately, to form close-packed two-dimensional nanoparticle arrays by covalent bonding.