A commercial SERS substrate does not only require strong enhancement, but also can be reused and recycled in actual application. Herein, Fe3O4/SiO2/ZnO/Ag (FSZA) have been synthesised, which consisted of Fe3O4 core with strong magnetic field response and an intermediate SiO2 layer as an electronic barrier to keep the stability of magnetite particles and outer ZnO and Ag as the effective layers for detecting pollutants. The SERS enhancement factor (EF) of the FSZA was ~8.2 × 105. The enhancement mechanism of the FSZA core-shell microspheres were anatomized. The electromagnetic enhancement of surface deposited Ag, charge transfer, and molecular and exciton resonances act together to cause such high enhancement factors. For practical application, the FSZA core-shell microspheres were also used to detect thiram, moreover, which was collected and separated by an external magnetic field, and maintained the SERS activity without significant decline during multiple tests. So the good enhancement performance and magnetic recyclability make the FSZA core-shell microspheres a promising candidates for practical SERS detection applications.