Patterned nanoparticle arrays on solid surface have drawn much attention because of their potential for fabricating nanoelectronic devices. Here, we report a novel method to realize the site selective assembly of gold nanoparticles on silicon, which combines the AFM nano oxidation technique and wet chemical assembly technique. Nanosized oxide dots were generated by AFM nano oxidation on OTS covered silicon, followed by modification of APTMS monolayer on the oxide dots. Because of the specific electrostatic attraction between gold nanoparticles and the amino terminated APTMS monolayers, gold nanoparticles were only deposited on the oxidized regions. With this approach, we have successfully fabricated site selective gold nanoparticle assemblies.