It is a challenging and valuable work to synthesize surface enhanced Raman scattering (SERS) substrate with low cost and high performance by simple methods, and use it to detect pesticide residues in food. Here, Ferrero® chocolate-like Cu2O@Ag microspheres (FRC-Cu2O@Ag) were fabricated by a facile in-situ redox reaction. Cu2O directly acted as templates and reducing agents to induce the nucleation and growth of Ag nanoparticles on the microspheres surfaces. The prepared semiconductor-noble metal hybrids of Cu2O@Ag were utilized as SERS substrates to detect 4-mercaptobenzoic acid (4-MBA) and thiram molecules. The distinguished SERS effect was achieved when target molecules absorbed on the FRC-Cu2O@Ag composite. The substrate presented excellent sensitivity and reproducibility for the detection of 4-MBA and thiram with the limit of 10−10 and 10−9 M, respectively. Due to combining both advantages of electromagnetic enhancement of Ag metals and chemical enhancement of Cu2O semiconductors, the obtained FRC-Cu2O@Ag microspheres provided a SERS platform to conveniently detect molecules with thiol groups. When it was applied to detect thiram residues on apple peel and the detection limit was 1.2 × 10−7 M, low than maximal residue limit (MRL) of 7 × 10−6 M in fruit prescribed by the U.S. Environmental Protection Agency (EPA).