In this paper, a detection strategy based on Surface-enhanced Raman Scattering (SERS) was proposed to quickly and simply separate target molecules from samples. Fe3O4@SiO2@Ag (FSA) magnetic particles modified with flower-like silver nanosheets were employed for efficient enrichment of target molecules, followed by their self-assembly onto the NdFeB substrate surface in fluid medium. The SERS sensitivity was indirectly adjusted by changing the reaction time to control the morphology of flower-like silver nanosheets on the surface of magnetic particles. SERS experiment showed that the substrate prepared by this detection strategy had high sensitivity, Rhodamine 6G (R6G) could be detected at the concentration of 10−8M and Methylene Blue (MB) could be detected at the concentration of 10−7M, the calculated enhancement factor was 1.34 × 105. In addition, the uniformity of the substrate was evaluated by SERS mapping using 10-6 M R6G, the RSD value of 8.89% was obtained. This detection strategy provides a new idea for simple and rapid SERS detection of organic dye.