Plasmons have facilitated diverse analytical applications due to the boosting signal detectability by hot spots. In practical applications, it is crucial to fabricate straightforward, large-scale, and reproducible plasmonic substrates. Dewetting treatment, via applying direct thermal annealing of metal films, has been used as a straightforward method in the fabrication of such plasmonic nanostructures. However, tailoring the evolution of the dewetting process of metal films poses considerable experimental complexities, mainly due to nanoscale structure formation. Here, we use grazing-incidence small- and wide-angle X-ray scattering for the in situ investigation of the high-power impulse magnetron sputter deposition of Ag on self-assembled Au nanoparticle arrays at low-temperature dewetting conditions. This approach allows us to examine both the direct formation of binary Au/Ag nanostructure and the consequential impact of the dewetting process on the spatial arrangement of the bimetallic nanoparticles. It is observed that the dewetting at 100 °C is sufficient to favor the establishment of a homogenized structural configuration of bimetallic nanostructures, which is beneficial for localized surface plasmon resonances (LSPRs). The fabricated metal nanostructures show potential application for the surface-enhanced Raman scattering (SERS) detection of rhodamine 6G molecules. As SERS platform, bimetallic nanostructures formed with dewetting conditions turn out to be superior to those without dewetting conditions. The method in this work is envisioned as a facile strategy for the fabrication of plasmonic nanostructures.