Surface-enhanced Raman scattering (SERS) has gained significant attention in various fields, including biomedical diagnostics, environmental monitoring, and food safety. This technique offers many advantages such as label-free detection and the ability to detect analytes at low concentrations. In this study, we present a variety of tungsten oxide (W18O49) microstructures as solid SERS substrates using various solvents realized by a simple hydrothermal approach. Among them, the well-defined sea urchin-like W18O49 microstructures support greater light scattering and confinement to enhance the SERS signal when compared to other W18O49 structures. The surface of well-defined sea urchin-like W18O49 microstructures was then modified with uniformly distributed silver nanoparticles (Ag NPs). The combination of the unique morphology of the Ag and sea urchin-like W18O49 microstructures (W18O49@Ag) led to improved detection capabilities for analytes such as rhodamine 6 G (R6G) and thiram molecules. The SERS enhancement factor (EF) of sea urchin-like W18O49@Ag microstructures was estimated to be as high as 1.53×106 with the lowest detectable concentrations of 1 nM and 1 μM for R6G and thiram, respectively. Thus, the well-defined sea urchin-like W18O49@Ag microstructures are excellent choice to replace the pure noble metal SERS substrates in the fields of rapid detection and trace analysis due to their high sensitivity, repeatability, and long-term stability.