Au nanoshells consisting of a dielectric core with a metallic layer of nanometer thickness exhibit tunable local surface plasmon resonance property. The core size has a great effect on the aggregation state of formed Au nanoshells, which leads to the variation of the intensity of surface enhanced Raman scattering (SERS). This paper reports a controllable aggregation for the fabrication of Au nanoshells with different size of core. TEM results demonstrated that formed Au nanoshells showed obvious aggregation with decreasing the size of core. By SERS analysis, different aggregation state leads to different SERS signal intensity. By comparison, Au nanoshells with core size of 50–80 nm exhibit high SERS enhancement effect.