Plasmonic molecules, which are geometrically well-defined plasmonic metal nanoparticle clusters, have attracted significant attention due to their enhancement of light–matter interactions owing to a stronger electric field enhancement than that by single particles. High-resolution lithography techniques provide precise positioning of plasmonic nanoparticles, but their fabrication costs are excessively high. In this study, we propose a lithography-free, self-assembly fabrication method, termed the dual-dewetting process, which allows the control of the size and density of gold nanoparticles. This process involves depositing a gold thin film on a substrate and inducing dewetting through thermal annealing, followed by a second deposition and annealing. The method achieves a uniform distribution of particle size and density, along with increased particle density, across a 6-inch wafer. The superiority of the method is confirmed by a 30-fold increase in the signal intensity of surface-enhanced Raman scattering following the additional dewetting with an 8 nm film, compared to single dewetting alone. Our findings indicate that the dual-dewetting method provides a simple and efficient approach to enable a variety of plasmonic applications through efficient plasmonic molecule large-area fabrication.