Although mesocrystals with ordered building units have great potential in many fields because of the large amount of organic molecules used as structure-directing agents during their synthesis process, severe matrix interference makes their surface-enhanced Raman scattering (SERS) properties rarely understood. Herein, a rapid (20 s) and green microwave synthetic route is developed for the 100 g scale preparation of plasmonic W18O49 mesocrystals with no additives. The ultrathin (1.5 nm) and oxygen vacancy-rich W18O49 nanowires as a building unit greatly improve the interface charge transfer, while the periodic mesocrystal structure significantly enhances the localized surface plasmon resonance effect and creates high-density electromagnetic hot spots among the nanowires. An outstanding enhancement factor of 1.2 × 107 and an ultralow detectable limit of 10-11 M are achieved, and the single-molecule imaging is also realized on this mesocrystal-based SERS substrate. Moreover, the relative standard deviation of the fabricated large-area (2.2 cm2) SERS substrate is only 6.8%.