Arrayed resonant cavity with outstanding optical trapping ability have received increasing attention in surface-enhanced Raman spectroscopy (SERS). Here, a three-dimensional (3D) composite AgNPs-Al2O3/Au/inverted patterned sapphire substrate PMMA (IPSSPMMA) flexible resonant cavity system is theoretically and experimentally investigated as a flexible SERS sensor. With the help of an effective plasma coupling (localized surface plasmons (LSPs) and surface plasmon polaritons (SPPs)), as shown by the Finite Element Method, a resonant cavity between IPSSPMMA and a particle-film nanostructure is created. Moreover, the proposed fabrication scheme can be easily used for large-scale fabrication. To measure the performance of IPSSPMMA, Rhodamine 6 G (R6G) and Crystalline violet (CV) were used as probe molecules with limit of detection (LOD) of 6.01 × 10-12 M and 5.36 × 10-10 M, respectively, and enhancement factors (EF) of R6G up to 8.6 × 109. Besides, in-situ detection of CV on the surface of aquatic products with a LOD of 3.96 × 10-5 M, enables highly sensitive in-situ detection of surface analytes. The Raman performance and in-situ detection results demonstrate that the proposed flexible compositing resonant cavity system has the advantages of ultra-sensitivity, stability, uniformity, and reproducibility, and has great potential for applications in the food safety field.