A flexible paper base SERS substrate with hydrophobic surface was fabricated through a simple route. The Ag nanoparticle was modified on filter paper through in situ growth method. After optimizing the condition during the growth and surface modification process, the hydrophobic filter paper-Ag was prepared via soaking in 10-8 g/ml of 1-Dodecanethiol with 12 h growth time. The flexible SERS substrate exhibit excellent hydrophobic properties, the contact angle of water could achieve 130.2 °. When the solution of analyte was dropped onto the SERS substrate, the diffusion effect was limited. After evaporation, the target analyte was concentrated within a fixed area. The hydrophobic SERS substrate could simultaneously improve the SERS signal and fluorescence of the analyte. The paper base SERS substrate with hydrophobic surface was used for detecting thiram from edible oil, and the sensitivity was down to 10-7 M. We proposed a flexible, economical and green hydrophobic SERS substrate for the detection of harmful ingredient from hydrophobic phase.