Surface-enhanced Raman spectroscopy (SERS) has attracted increasing interest for chemical and biochemical sensing. Several studies have shown that SERS intensities are significantly increased when an optical interference substrate composed of a dielectric spacer and a reflector is used as a supporting substrate. However, the origin of this additional enhancement has not been systematically studied. In this paper, high sensitivity SERS substrates composed of self-assembled core-satellite nanostructures and silica-coated silicon interference layers have been developed. Their SERS enhancement is shown to be a function of the thickness of silica spacer on a more reflective silicon substrate. Finite difference time domain modeling is presented to show that the SERS enhancement is due to a spacer contribution via a sign change of the reflection coefficients at the interfaces. The magnitude of the local-field enhancement is defined by the interference of light reflected from the silica-air and silica-silicon interfaces, which constructively added at the hot spots providing a possibility to maximize intensity in the nanogaps between the self-assembled nanoparticles by changing the thickness of silica layer. The core-satellite assemblies on a 135 nm silica-coated silicon substrate exhibit a SERS activity of approximately 13 times higher than the glass substrate.