Surface‐enhanced Raman spectroscopy (SERS) has a wide range of applications in molecular recognition, environmental pollutant detection, and other fields. However, the intensity and number of “hot spots” in 1D and 2D nanostructures are limited due to the scale‐dependent localized plasmonic effect of nanostructures, making it difficult to increase the detection limit. Herein, a kind of 3D substrate called Au@Ag double‐layer nanoarray (Au@Ag DLA) is prepared using rapid thermal annealing and chemical replacement methods. The energy‐dispersive spectrometer spectra confirm the successful growth of AgNPs on the gold nanoarray (Au SLA) by showing no presence of the copper element, indicating complete replacement of the Cu film deposited on Au SLA by Ag atoms. The detection limit of malachite green in Au@Ag DLA is 10−8 mol L−1, four and three orders of magnitude higher than that of Au SLA and AgNPs, respectively. This stronger SERS effect of Au@Ag DLA arises from the larger number of intense hot spots generated not only on the horizontal surface but also in the vertical direction. This finding provides a method for developing efficient and stable 3D SERS substrate, which can be utilized for the trace detection of water pollutants and pesticide residue.