Surface-enhanced Raman spectroscopy (SERS) provides a fast, simple, and label-free approach that can directly detect various analytes attached to SERS substrates and provide qualitative and quantitative information based on the SERS spectra of the analyte. The signal enhancement provided by noble metal particles allows us to achieve high sensitivity and good stability even at low concentrations in water quality testing. Over the past decade, SERS has become increasingly popular in the detection field, highlighting its significant application potential. However, the signal enhancement of single AuNPs is inferior to that of AgNPs, but we can achieve an overall enhancement by uniformly arranging multiple AuNPs. The hot-spot effect, which is crucial for Raman signal enhancement, occurs only when NMNPs are within a specific distance. However, when noble metal particles come into contact with each other, the enhancement effect of the hot spot disappears. Therefore, in this study, AuNPs@MPS-SH substrates with surface-enhanced Raman scattering (SERS) activity were successfully synthesized by immobilizing AuNPs on thiol-functionalized mesoporous silica (MPS-SH). MPS nanospheres with tailored pore size and surface-bound -SH groups were synthesized for the controlled embedding of Au nanoparticles (AuNPs). By adjusting the ratio of reactants, uniform AuNP dispersion and strong MPS-AuNP interactions were achieved. This optimized structure creates localized surface plasmon resonance (LSPR) hotspots, significantly enhancing the surface-enhanced Raman scattering (SERS) effect for ultrasensitive analyte detection. Transmission electron microscopy (TEM) revealed that the average diameter of MPS nanoparticles is 260 nm, with a pore size of 8 nm. Optimal Raman enhancement was achieved at an AuNPs concentration of 2.6 × 1018 particles/mL. The lowest detection limit concentration for Rhodamine 6G was below 10−6 M, while for uremic toxin (urea) it was below 10−3 M. The ability to directly detect low concentrations by mixing with the analyte demonstrates the ultra-high sensitivity and label-free detection potential of this study in the fields of water quality and disease detection.