Owing to their nanoscale size and porous structure, both colloidal gold nanoparticles (AuNPs) and nanoporous gold (NPG) have demonstrated good and stable surface-enhanced Raman scattering (SERS) activity, and are therefore widely used as SERS substrates for the rapid detection of various components in food, environmental, biological, and other samples. In this study, we fabricated a novel, sensitive, and reproducible composite three-dimensional (3D) substrate for rapid SERS-based detection of illegal additives in food products. AuNPs and NPGs were prepared by chemical reduction and chemical dealloying methods, with the particle size of AuNPs about 60 nm and the pore size of NPG in the range of 5–36 nm. The AuNPs were then assembled on the surface of NPG to form the composite substrate 3D-NPG/AuNPs, which was characterized by transmission electron microscopy, scanning electron microscopy, X-ray diffraction, and other methods. Finally, the new SERS substrate combined with a portable Raman spectrometer was used to detect the illegal food additives 6-benzylaminopurine and melamine, with detection limits of 1 × 10−9 M and 5 × 10−7 M respectively. We further analyzed the relationship between the dealloying time-controlled morphology and the SERS properties of NPG, demonstrating that 3D-NPG/AuNPs as a novel SERS substrate have strong practical application potential in the rapid detection of food additives and other substances.