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A sensitive and simple method for detecting Cu²⁺ in the water source was proposed by using surface-enhanced Raman scattering spectroscopy (SERS) based on the Ag@SiO₂/Au core–shell composite. The Ag@SiO₂ SERS tag was synthesized by a simple approach, in which Ag nanoparticles were first embedded with Raman reporter PATP and next coated with a SiO₂ shell. The Ag@SiO₂ nanoparticles had strong stability even in a high-concentration salty solution, and there were no changes to their properties and appearance within one month. The Ag@SiO₂/Au composite was fabricated through a controllable self-assemble process. L-cysteine was decorated on the surface of a functionalized Ag@SiO₂/Au composite, as the amino and carboxyl groups of it can form coordinate covalent bond with Cu²⁺, which shows that the Ag@SiO₂/Au composite labelled with L-cysteine has excellent performance for the detection of Cu²⁺ in aqueous media. In this study, the SERS detection of Cu²⁺ was carried out using Ag@SiO₂ nanoparticles, and the limit of detection (LOD) as low as 0.1 mg/L was achieved.