Residual pesticides in vegetables or fruits have been become one of the world’s most concerned food safety issues. Au-Ag core-shell nanoparticles (Au@Ag NPs) coupled with surface-enhanced Raman spectroscopy (SERS) was used for analysis of flusilazole which was widely applied in pears. Three different diameters of Au@Ag NPs were prepared to select the best SERS substrate for analyzing flusilazole. The Au@Ag NPs sizes of 90 ± 7 nm showed the highest enhancement effect and could be detected flusilazole standard solution and the minimum detectable concentration was 0.1 mg/L. Flusilazole in pear could also identified at as low as 0.1 μg/g. The amount of adsorbent is critical in the sample preparation process and the best amount of each absorber dosage was 0.6 g MgSO₄, 0.2 g C₁₈ and 0.2 g primary secondary amine (PSA). The experimental results indicated a good linear relationship between the Raman intensities of chief peaks and the concentrations of flusilazole solutions (R² = 0.924–0.962). This study shows that Au@Ag as SERS substrate has great potential to analyze of flusilazole in food matrices.