Gap-enhanced Raman tags (GERTs) with built-in Raman molecules show excellent surface-enhanced Raman scattering (SERS) performance and great potential for biomedical applications. In this work, we add a silver (Ag) shell to gold (Au) single-shell GERTs (Au@BDT@Au) to form Au-Ag hybrid multi-shell nanoparticles. It is found that this modification enhances the SERS performance of the NPs and that the thickness of the Ag shell is a key factor in determining the enhancement. Double-shell bimetallic GERTs with a Au core, Au shell and exterior 2 nm-thickness silver shell (Au@BDT@Au@BDT@Ag) show the best SERS performance and good photostability. Moreover, we utilize the double-shell bimetallic GERTs to develop a new kind of SERS-based lateral flow immunoassay (LFIA), acheiving limit of detection as low as 0.7 mIU/mL (0.077 ng/mL). We demonstrated a simple way to fabricate sub-100 nm multi-shell bimetallic GERTs for use as SERS probes with strong Raman signals with potential for in vivo and in vitro application as bioimaging and biosensing probes.