The current article discusses surface-enhanced Raman spectroscopy (SERS) as a powerful technique for detecting molecules or ions by analyzing their molecular vibration signals for fingerprint peak recognition. We utilized a patterned sapphire substrate (PSS) featuring periodic micron cone arrays. Subsequently, we prepared a three-dimensional (3D) PSS-loaded regular Ag nanobowls (AgNBs) array using self-assembly and surface galvanic displacement reactions based on polystyrene (PS) nanospheres. The SERS performance and structure of the nanobowl arrays were optimized by manipulating the reaction time. We discovered that the PSS substrates featuring periodic patterns exhibited superior light-trapping effects compared to the planar substrates. The SERS performance of the prepared AgNBs-PSS substrates was tested under the optimized experimental parameters with 4-mercaptobenzoic acid (4-MBA) as the probe molecule, and the enhancement factor (EF) was calculated to be 8.96 × 104. Finite-difference time-domain (FDTD) simulations were conducted to explain that the AgNBs arrays’ hot spots were distributed at the bowl wall locations. Overall, the current research offers a potential route for developing high-performance, low-cost 3D SERS substrates.