We developed a highly sensitive and stable SERS-active substrate of Au@Ag@Ag core/shell/shell nanorods, formed by encapsulating Au nanorods (Au NRs) into a bilayer silver shell with Raman reporter molecules (4-mercaptobenzoic acid (4-MBA) and thiram) in the shell-shell gap. The core/shell/shell nanostructures demonstrated a high SERS enhancement and easy assembly. The important role of the bilayer silver shell in boosting the SERS intensity and detection sensitivity was revealed by comparing the performances of the Au@Ag@4-MBA@Ag NRs, Au@Ag@4-MBA NRs, and Au@4-MBA NRs. The obtained Au@Ag@4-MBA@Ag NRs exhibited a significantly promoted SERS intensity, which could reach around 2.6 times and 240 times that of the Au@Ag@4-MBA NRs and Au@4-MBA NRs, where the enhancement factor was found to be strongly correlated with the shell thickness. The controllable plasma properties and SERS effect of the Au@Ag@4-MBA@Ag NRs could be optimized by adjusting the dose of silver nitrate. The SERS substrate comprising core/shell/shell nanorods was highly reproducible and stable (retaining 83% SERS intensity after one month). Moreover, the highly sensitive detection of the pesticide thiram with a detection limit as low as 1.74 × 10-9 M was achieved by taking advantage of the great SERS response of the core/shell/shell nanostructures, which was 1-2 orders of magnitude lower than for other SERS substrates. The developed SERS substrate could be readily extended to embed other target analytes into the core/shell/shell nanostructure for novel and sensitive detection. This study could enable fresh approaches toward next-generation ultrasensitive analyte detection.