We have successfully prepared a highly sensitive sandwich nanosensor combined Fe3O4 and Au@ATP@Ag nanorods for histamine detection based on surface-enhanced Raman spectroscopy (SERS). The Fe3O4 beads with –COOH served as a capture part to enrich histamine. The Au@ATP@Ag core-shell nanorods functionalized with Nalpha,Nalpha-Bis(carboxymethyl)-l-lysine (AB-NTA) were then used to connect with the imidazolyl group of histamine, simultaneously the internal standard 4-aminothiophenol (4-ATP) in the core-shell structure was used as the SERS signal. PLS regression model based on concentration range 10−3-10−8mol/L showed a linear trend with R2 = 0.9907. Our new approach can quickly and reliably determine histamine in fish sample and RAW264.7 cell lysates. This protocol for histamine extraction and SERS analysis enables the development of ultra-sensitive method for histamine detection. The scheme of histamine detection procedure. Display omitted •We proposed Fe3O4/Au@ATP@Ag Nanorod sandwich structure integrated separation and detection for histamine in fish and RAW264.7.•Ultra-sensitive quantitative detection of histamine in 10−3-10−8 M and R2 = 0.9907.•Indirect measurement of histamine using internal standard 4-ATP signal of core-shell structure to avoid interference.•Fe3O4 quickly separate histamine from fish and RAW264.7 cell lysates by magnets without tedious procedures.