Surface-enhanced Raman scattering (SERS) is an efficient method for substance detection. Unlike conventional Raman scattering, whose signal is too weak to be detected, SERS has been widely used in many applications due to its superior merits of high sensitivity. Priori knowledge of SERS substrate characteristics contributes to improve the performance of the prepared SERS substrate. In this paper, SERS substrate on the basis of Au@PS array was prepared using lon sputtering coating. The size and clearance of the sphere were controlled by adjusting the coating thickness. Performance and surface features of a variety of SERS substrates with different coating thickness were studied. SEM results indicate that gold particles on the outside surface membrane layer are obviously visible when the coating thickness is 50 nm. Subsequently, Raman characteristics of the prepared substrate were valued by using Rhodamine 6G. Results show that the SERS substrate with a coating thickness of 50 nm has the strongest enhancement effect. Simulations were also carried out to get a better knowledge of the electromagnetic field distribution within the prepared SERS substrate. Results of FDTD simulation show that the electromagnetic of the clearance and field near the gold particles is strong. And meanwhile, the intensity of the electromagnetic field is the strongest when the coating thickness is equal to 50 nm, which is in agreement with the experimental results.