Plasmonic silver nanoparticles (AgNPs) arranged on polyimide (PI) nanopillars (AgNP/PI) were developed as a stable photothermal surface-enhanced Raman spectroscopy (SERS) platform. The AgNP/PI substrates were prepared via maskless plasma etching and metal deposition using an in situ vacuum sputtering system. The AgNP/PI with high periodicity and high areal density led to high sensitivity, with a SERS enhancement factor (EF) of 2.2 × 108, and excellent reproducibility (relative standard deviation of 7.6%), as evaluated using the high-precision Raman mapping technique. To support the high SERS EF and sensitivity, the near-field enhancements of the dense AgNP array were calculated using a finite-difference time domain method. Notably, compared with AgNPs on polyethylene terephthalate (PET) nanopillar substrates, the AgNPs formed on the thermally stable PI nanopillar substrates exhibited excellent photothermal stability under illumination with a high-powered laser. The PI and PET surface changes induced by photoinduced local heating were investigated in terms of the glass-transition temperature, coefficient of thermal expansion, and thermal conductivity. The new plasmonic SERS platform has strong potential for reliable molecular detection in practical sensing applications with high-powered laser illuminations. Display omitted •Ag nanoparticles coated onto polyimide for SERS were prepared via in situ sputter-etching and deposition processes.•Designed dense hotspots generate reproducible and reliable SERS signals for practical diagnoses.•The excellent thermal properties of PI prevent thermally induced damage such as structural deformation and decomposition.