This paper provides a convenient and simple method for fabricating a self-organized two-dimensional (2D) array of gold nanoparticles on a silicon substrate. The silicon substrate, modified with an aminopropyltriethoxylsilane(APTES) monolayer, was first exposed to a gold colloidal suspension to deposit the gold particles and form a submonolayer of gold nanoparticles. This was followed by treatment with an alkanethiol solution, and then this randomly scattered submonolayer of nanosized gold particles on the silicon substrate was organized into small patches of 2D nanoparticle aggregates. Finally an alcohol solvent was used to drive these small patches of gold nanoparticle aggregates to self-organize together and form continuous ordered arrays on the silicon surface. The SEM images of the samples show that ordered two-dimensional arrays of gold nanoparticles are formed over a very large area and that the nanoparticles are highly organized and formed hexagonally closed packed structured arrays. This highly organized structure of gold nanoparticles can be reproduced over a large area by these effective procedures. Therefore, it is believed such procedures hold promise as an advanced new approach to construct ordered mesoscopic structural materials or for the controlled self-assembly of nanoparticles and could provide the possibility of detecting the collective physical properties of the ensemble.