Pesticide residues in agricultural products and environmental water pose significant threats to human health and ecosystems. The urgent need for rapid detection and degradation of complex samples containing multiple pesticides has driven advancements in detection methods. Surface-Enhanced Raman Spectroscopy (SERS), a powerful molecular detection technique, has attracted considerable attention in food safety, environmental monitoring, and biological analysis due to its unparalleled sensitivity, non-destructive characterization capabilities, and high specificity. In this study, we presented a SERS detection substrate based on filter paper incorporating Ag nanoparticles (AgNPs) and ZnO nanoparticles (ZnONPs). This innovative SERS substrate enables sensitive and recyclable detection of deltamethrin and atrazine pesticides. The detection limits for bromopropylate and atrazine were 38.87 μg/L and 39.35 μg/L, respectively. The method's detection limits meet the groundwater quality standards for allowable limits in agricultural water use. Notably, the paper-based SERS substrate achieved rapid degradation of pollutants within 10 min under UV light exposure, demonstrating its efficacy. Even after five consecutive uses, the substrate maintained its capability to detect various pesticides within mixed samples. This study explores the application of paper-based SERS detection technology in the investigation of pesticide degradation mechanisms and kinetics, discussing the effects of environmental conditions such as pH and temperature on the experimental results. The experimental findings support the theoretical research. Additionally, density functional theory (DFT) models were used to study the hydrolysis evolution mechanisms of two pesticides under different pH conditions. Our study highlights that paper-based SERS detection technology is an effective method for studying the degradation mechanisms of pesticides. This innovative approach advances the understanding of pesticide degradation processes and opens avenues for further exploration.