A SERS substrate FP/Ag/ZIF-8 composed of filter paper (FP), silver nanoparticles (AgNPs) and zeolitic imidazolate framework (ZIF-8) film arranged in a layered structure was developed for sensitive detection of pesticide thiram in various samples. Roles of these components in analyte adsorption and Raman signal enhancement were studied using a pesticide intermediate 4-Aminothiophenol (4-ATP) as the probe. The substrate showed high adsorption and optimized SERS response with thick metal organic framework (MOF) coating (125 nm), which is different from previous reported plasmonic particle-MOF composite substrate, where thinnest MOF coating produced the strongest SERS signal. Detection limit for 4-ATP improved 1000-fold on FP/Ag/ZIF-8 (3 pM) compared with that on FP/Ag (3 nM). Importantly, the FP/Ag/ZIF-8 with porous and flexible property can efficiently capture pesticide thiram in different real samples using soaking, filtration or swabbing operation. The subsequent SERS detection of thiram showed advantages of low detection limit (soaking, LOD: 0.04 nM in lake water), fast detection (filtration, within 1 min in peach juice) and suitable for curve surface analysis (swabbing, LOD: 0.1 ng/cm on apple peel), respectively. The substrate also displayed good reproducibility, high stability and size-selective response for thiram detection. Such a layered plasmonic particle/MOF hybrid may hold great promise for toxicant analysis in environment and food.