Biosensors are novel devices for offering fast, point of care results in healthcare fields. Nanostructures can improve the performance of biosensors. For example, plasmonic gold nanohole arrays have been demonstrated to amplify the surface-enhanced Raman scattering (SERS) signal in biosensors because of their unique optical properties and highly tunable localized surface plasmon resonance (LSPR). However, it remains a challenge to fabricate nanostructures such as nanohole arrays. Herein a gold nanohole array-silica spacer-gold nanodisk array has been fabricated based on nanosphere lithography. The SERS effect is considerably improved due to the plasmonic coupling between the gold nanohole array and the nanodisk array separated by a small silica gap (~10 nm). Ultraviolet-visible spectroscopy, Raman spectroscopy, and finite-difference time domain simulations have been used to characterize the performance. The plasmonic nanostructure obtained can be potentially integrated into microfluidic devices for healthcare and environmental monitoring.