In this report, we fabricated the multi-layer Ag/Fe/Ag sandwich cap-shaped films on monolayer nonclosed packed (ncp) polystyrene colloidal particle (PSCP) templates through a layer-by-layer (LBL) depositing method. This research focused on the surface-enhanced Raman scattering (SERS) effect of the thickness of the deposited Fe film which was controlled by the sputtering time. The SERS intensities were increased firstly, and then decreased as the thickness of Fe layer grows gradually, which is attributed to the charge transition from the Fermi level of the Ag NPs to Fe layer. The use of multi-layer Ag/Fe/Ag sandwich cap-shaped films enables us to evaluate the contribution of surface plasmon resonance and charge distribution between Ag and Fe to SERS enhancement. Our work introduced a novel system (Ag/Fe/Ag) for high performance SERS and extended the SERS application of Fe. Furthermore, we have designed the Ag/Fe/Ag SERS-active substrate as the immunoassay chip for quantitative determination of AFP-L3 which is the biomarker of hepatocellular carcinoma (HCC). The proposed research demonstrates that the SERS substrates with Ag/Fe/Ag sandwich cap-shaped arrays have a high sensitivity for bioassay. (C) 2017 Elsevier B.V. All rights reserved.