A series of Au@Ag core–shell nanocomposites with varying Ag shell thickness were prepared as potential SERS substrates via chemical reduction method. Rhodamine 6G, crystal violet, and thiram were selected as probes for SERS substrate optimization and sensitivity testing of nanocomposites. According to the results, the Au surface was uniformly coated with a ∼3–12 nm thick Ag layer, exhibiting the even particle size distribution. The above nanocomposites demonstrated an extremely high detection limit for Rhodamine 6G (up to 10−11 M) within a sensitivity range of 10−5 to 10−11 M. At the same time, the detection limits for crystal violet and thiram were 10−10 M and 10−9 M, respectively. Moreover, the SERS performance remained basically unchanged after 30-day storage, indicating good stability and uniformity of Au@Ag substrates. Thus, the proposed Au@Ag nanocomposites have a great application potential for the detection of low-concentration pollutants in the environment along with the prolonged in-use stability.