Flexible surface-enhanced Raman scattering (SERS) has received considerable attention in the field of rapid analysis. However, obtaining accurate quantitative SERS results remains challenging. Here, we develop a SERS sensor based on self-assembly and mask-assisted techniques for the precise transfer of Au@PB@Ag nanoarrays onto filter paper. Prussian blue (PB) as an internal standard (IS) is used to calibrate the fluctuations in the SERS signal induced by the microstructure of the filter paper, and can generate a local plasmon resonance under a Raman laser at a wavelength of 633 nm, which enables a dual electromagnetic enhancement of the internal self-calibration and external target molecule signals. The SERS substrate has a low limit of detection of 3.96 × 10