Fe3O4 nanoparticles were first modified with tetraethoxylsilane to form Fe3O4/SiO2 nanoparticles, followed by the addition of 3-aminopropyltriethoxysilane and 3-thiolpropyltriethoxysilane to introduce –NH2 and –SH groups to the surface of Fe3O4/SiO2 nanoparticles. Gold nanoparticles were further assembled on the surface of Fe3O4/SiO2 via the electrostatic adsorption of –NH2 and the Au–S bond to produce stable core–shell Fe3O4/SiO2/Au gold/magnetic nanoparticles. These Fe3O4/SiO2/Au gold/magnetic nanoparticles were characterized by a variety of techniques such as transmission electron microscopy (TEM) and energy dispersive X-ray spectroscopy (EDX), and afterwards conjugated with tetrodotoxin antibodies (Ab) and used as a Raman active substrate (Fe3O4/SiO2/Au–Ab) with Rhodamine B (RhB)-labeled tetrodotoxin antibody as a Raman reporter (Ab–RhB). Upon mixing these reagents with tetrodotoxin (TTX), a sandwich complex [Fe3O4/SiO2/Au–Ab···TTX···Ab–RhB] was generated due to the specific antibody–antigen interactions. The immunocomplex was subsequently separated by an externally applied magnetic source and concentrated into a pellet point, where the laser interrogation of the pellet produced a strong signal characteristic of RhB. The logarithmic intensity of the signal was found to be proportional to the concentration of TTX with a limit of detection of 0.01 μg/mL and a detection linearity range of ~ 0.01–0.5 μg/mL. The established method eliminates the complicated procedures of traditional centrifuging, column separation, and incubation and achieves a rapid detection of tetrodotoxin with improved detection sensitivity.