Herein, a novel interference-free surface-enhanced Raman spectroscopy (SERS) strategy based on magnetic nanoparticles (MNPs) and aptamer-driven assemblies was proposed for the ultrasensitive detection of histamine. A core-satellite SERS aptasensor was constructed by combining aptamer-decorated Fe3O4@Au MNPs (as the recognize probe for histamine) and complementary DNA-modified silver nanoparticles carrying 4-mercaptobenzonitrile (4-MBN) (Ag@4-MBN@Ag-c-DNA) as the SERS signal probe for the indirect detection of histamine. Under an applied magnetic field in the absence of histamine, the assembly gave an intense Raman signal at “Raman biological-silent” region due to 4-MBN. In the presence of histamine, the Ag@4-MBN@Ag-c-DNA SERS-tag was released from the Fe3O4@Au MNPs, thus decreasing the SERS signal. Under optimal conditions, an ultra-low limit of detection of 0.65 × 10-3 ng/mL and a linear range 10-2–105 ng/mL on the SERS aptasensor were obtained. The histamine content in four food samples were analyzed using the SERS aptasensor, with the results consistent with those determined by high performance liquid chromatography. The present work highlights the merits of indirect strategies for the ultrasensitive and highly selective SERS detection of small biological molecules in complex matrices.