Surface-enhanced Raman scattering technology plays a prominent role in spectroscopy. By introducing plasmonic metals and photonic crystals as a substrate, SERS signals can achieve further enhancement. However, the conventional doping preparation methods of these SERS substrates are insufficient in terms of metal-loading capacity and the coupling strength between plasmonic metals and photonic crystals, both of which reduce the SERS activity and reproducibility of SERS substrates. In this work, we report an approach combining spin-coating, surface modification, and in situ reduction methods. Using this approach, a photonic crystal array of SiO2@Au core-shell structure nanoparticles was prepared as a SERS substrate (SiO2@Au NP array). To study the SERS properties of these substrates, Rhodamine 6G was employed as the probe molecule. Compared with a Au-SiO2 NP array prepared using doping methods, the SiO2@Au NP array presented better SERS properties, and it reproduced the SERS spectra after one month. The detection limit of the Rhodamine 6G on SiO2@Au NP array reached 1 × 10-8 mol/L; furthermore, the relative standard deviation (9.82%) of reproducibility and the enhancement factor (1.51 × 106) were evaluated. Our approach provides a new potential option for the preparation of SERS substrates and offers a potential advantage in trace contaminant detection, and nondestructive testing.