Montmorillonite (MMT) coated with roughened noble metal nanoparticles are novel hybrid nanocomposite with a wide range of applications including agriculture, materials science and biomedical engineering. Herein, we developed a hybrid nanocomposite (MMT/AgNPs) based on MMT coated with silver nanoparticles (AgNPs), which can be used as a cost-effective and efficient surface-enhanced Raman spectroscopy (SERS) substrate for the detection of pesticides in fruits and vegetables. MMT itself is negatively charged and can be assembled with positively charged AgNPs through electrostatic interactions. Moreover, MMT has a layered 2D structure that possesses a large surface area, which can load a large number of AgNPs to form more SERS hotspots for the ultrasensitive measurement. SERS performance of the MMT/AgNPs nanocomposite was tested by 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) and the substrate can obtain the strongest SERS enhancement effect with the volume ratio of MMT/AgNPs of 1 : 10. These substrates were applied in the measurement of thiram in apples and spinach samples by SERS. Detection limits of pesticide molecules of 5.0 × 10-8 M and 1.0 × 10-7 M in apples and spinach, respectively, were obtained. Most importantly, MMT nanosheets are a robust platform that allowed AgNPs to be evenly and thoroughly distributed and stabilized over the substrate, improving the repeatability and stability of SERS detection. These results reveal that the MMT/AgNPs nanocomposites are suitable substrates for the real-world SERS analysis of pesticide and other contaminants in complex food matrices.