ABSTRACT Surface‐enhanced Raman spectroscopy has emerged as a powerful tool for molecular detection, with 3D‐nanostructured substrates offering significant advantages in sensitivity enhancement and reproducibility. In this study, finite‐difference time‐domain methods were performed to optimize the design of 3D two‐layered Au nanocone SERS substrates. The electric (E) field distribution and enhancement were systematically analyzed for different nanocone configurations, including variations in the number of nanocones per layer. The results demonstrate that these substrates significantly amplify the E‐field intensity, primarily due to multiple plasmon coupling modes. Notably, the E‐field strength is approximately 1.5 times higher than that of the single primary Au nanocones. Furthermore, the simulations reveal that E hot spots are predominantly localized at the tips of the nanocones, where the highest field intensities are observed. These findings provide valuable insights for the rational design of high‐performance 3D SERS substrates and highlight the potential of two‐layered Au nanocone arrays for advanced molecular sensing applications.