Since the morphology and element composition of metal nanostructures strongly affect the surface plasma oscillation characteristics, it has been widely concerned in surface enhanced Raman scattering (SERS). Herein, we proposed a novel route to fabricate composite Au/Ag nanoparticle arrays with synergistic effect for electromagnetic enhancement. Ag nanoparticles were electrodeposited onto a home-made template with highly ordered bowl-like pits. After a novel method of “confined annealing”, we further achieved well-regulated spherical Ag NP arrays, and the composite Au/Ag nanoparticle arrays were finally obtained via in situ replacement. The fabricated composite nanostructures showed stable and sensitive surface enhanced Raman scattering (SERS) performance mainly due to the synergistic effect and abundant “hot spots”, with the enhancement factor (EF) of [Formula: see text] for crystal violet (CV) molecules. In addition, this simple and effective preparation process greatly improved the uniformity of three-dimensional nanostructures, providing a new idea for further improving the stability of SERS signals.