Structured surface-enhanced Raman scattering (SERS) substrates that integrate plasmonic nanoparticles with tunable localized surface plasmon resonances are ideal for constructing gap nanostructures with hotspots. However, it remains challenging to create controllable nanogaps between plasmonic nanoparticles. In this work, we propose a hybrid nanostructure that integrates a two-dimensional periodic nanopillar array (PNA) with metal nanoparticle assemblies to regulate the spatial arrangement of hotspots and electromagnetic field coupling modes. Approximately 5-nm nanogaps were fabricated via reactive ion etching and subsequent Au deposition via magnetron sputtering. At the same time, the PNA periodicity was controlled by dual-beam interference lithography to match the laser excitation wavelength with the structure's optical resonance. The resulting high-density hotspots reduce molecular adsorption positional sensitivity, leading to enhanced reproducibility for rhodamine 6G with a relative standard deviation of 11.6%. Furthermore, the substrate achieves detection limits of 10, 1, and 100 nM for 4-nitrobenzenethiol, thiram and melamine molecules, respectively.