Thermally evaporated 10 nm-Ni/1 nm-Au/(30 nm-poly)Si structures were fabricated in order to investigate the thermal stability of Au-inserted nickel silicide. The silicide samples underwent rapid thermal annealing at 300~1100˚C for 40 seconds. The sheet resistance was measured using a four-point probe. A scanning electron microscope and a transmission electron microscope were used to determine the cross-sectional structure and surface image. High-resolution X-ray diffraction and a scanning probe microscope were employed for the phase and surface roughness. According to sheet resistance and XRD analyses, nickel silicide with Au had no effect on widening the NiSi stabilization temperature region. Au-inserted nickel silicide on a single crystal silicon substrate showed nano-dots due to the preferred growth and a self-arranged agglomerate nano phase due to agglomeration. It was possible to tune the characteristic size of the agglomerate phase with silicidation temperatures. The nano-thick Au-insertion was shown to lead to self-arranged microstructures of nickel silicide.