The application of a noble-metal-based plasmon-enhanced substrate to detect low-concentration analytes has attracted extensive attention. Most of the substrates used in recently reported researches are based on two-dimensional structures. Hence, we prepared a higher efficiency Raman activity substrate with a filter paper structure, which not only provides more plasmonic "hot spots," but also facilitates analyte extraction and detection due to the flexibility of the paper. The preparation of the plasmonic paper substrate adopted centrifugation to deposit the alloy nanoparticles onto the paper base. The optimal particle deposition condition was found by adjusting the centrifugal force and centrifugation time. Then, the surface-enhanced Raman spectroscopy (SERS) performance of the substrate was enhanced by altering the plasmon resonance peak on the surface of the nanoparticles. The enhancement factor of this paper-based substrate was 1.55×107, with high detection uniformity (10-6 M, rhodamine 6G) and a low detection limit (10-11 M, rhodamine 6G). Then, we applied the SERS substrate to pesticide detection; the detection limit of the thiram reached 10-6 M. As a result, the simple and cost-effective paper-based SERS substrate obtained in this way has high detection performance for pesticides and can be used for rapid detection in the field, which is beneficial to food safety and environmental safety.