Three-dimensional heterostructures (3DHS) with controlled compositions and tuned properties are highly desired for fundamental studies and applications in optoelectronics, nanocatalysis, clean energy, and biomedicine. However, conventional nanostructure engineering is hindered by challenges such as poor structural control, time- and energy-intensive processes, the use of hazardous and expensive chemicals, and harsh conditions. Here, we report plasma-assisted epitaxy (PAE) engineering of a metal-organic 3DHS with extreme light-matter interaction for rapid single-molecule-level sensing. Plasmonic-active 3DHS composed of structure-tuned gold-silver core-shell nanoparticles (AuAgCSNPs) was precisely engineered using stable and scalable microplasma-enabled nanofabrication under ambient conditions. The engineered AuAgCSNP-based 3DHS possessed exceptional Raman enhancement under suitable laser excitation, leading to single-molecule detection of SARS-CoV-2 spike proteins in simulated human saliva via surface-enhanced Raman scattering (SERS). The developed plasma fabrication method allows the production of centimeter-scale SERS-active metal-organic 3DHS on disposable, flexible, lightweight, and cost-effective substrates, thereby opening a new avenue for next-generation biosensing, nanoelectronics, nanocatalysis, and biomedical applications.