This article describes a hydrophobic paper based substrate modified with gold and silver alloy nanoparticles, which has a high-density distribution of nanoparticles in the deposition range and high detection sensitivity. It has certain research significance in the field of trace detection. Firstly, different proportions of gold and silver alloy nanoparticles were assembled onto a hydrophobic treated filter paper to improve the plasmonic properties of the substrate. At the same time, high-density nanoparticles were deposited onto a hydrophobic paper substrate through cyclic stacking of the deposition process. In the field of trace detection, the detection limit of trace Rhodamine 6G and crystal violet probe molecular solutions can reach 10-10 M and 10-8 M respectively, and this substrate can be used in the field of pesticide molecular detection, and its detection limit for thiram can reach 10-7 M.