In this paper, Fe3O4 nanoparticles were synthesized by solvothermal method and uniform silver-coated gold nanoparticles (Au@Ag NPs) were synthesized via seed growth through consecutive two-step reactions. Subsequently, Au@Ag NPs were assembled on the surface of Fe3O4 NPs functionalized with PEI due to the bond between -NH2 and Ag. We have regulated the SERS behavior of Fe3O4/Au@Ag NPs by adjusting the addition amount of Au@Ag. This Au@Ag NPs were characterized by Ultraviolet-visible (UV-vis) extinction spectroscopy. From the measurement of UV-vis spectra we can see that Au@Ag has a wide range of plasmon resonance from ca. 320 to 560 nm while one significant peak were observed at 530 nm for the Au NPs. This Fe3O4/Au@Ag NPs were systematically characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), vibrating sample magnetometer (VSM) and surface enhanced Raman spectroscopy (SERS). The SEM and TEM observation showed the NPs are highly monodispersive. The magnetic hysteresis loops showed the saturation magnetization (Ms) values of Fe3O4 NPs and Fe3O4/Au@Ag NPs are about 83.6 emu·g-1 and 57.1 emu·g-1, respectively. p-Aminothiophenol (p-ATP) molecules were employed to explore surface-enhanced Raman Spectroscopy (SERS) performance of Fe3O4/Au@Ag and showed excellent sensitivity to 2×10-9 mol/L. Simultaneously, Fe3O4@Au@Ag NPs were applied to the detection of thiram and showed sensitivity to 10-6 mol/L. Using these nanoprobes, analyte molecules can be easily captured, magnetically concentrated, and analyzed by SERS. In addition, the Fe3O4/Au@Ag NPs can be recycled with magnet, which exhibited great practical potentials.