The fine control of the nanogap and morphology of metal nanoparticles (NPs) has always been an obstacle, hindering the development and application of surface-enhanced Raman scattering (SERS) quantitative detection. Here, Au/4-mercaptobenzoic acid@Ag@Au-Ag bimetal core-shell nanocubes (NCs) with a “crescent arc” facet (C-Au/4MBA@Ag NCs) as a highly reliable and sensitive surface-enhanced Raman scattering SERS substrate is proposed for the first time. The bifunctional internal standard (IS) molecules (4MBA) govern the morphology of metal shells to maintain cubic configuration and provide calibration for SERS signals’ flotation. In parallel, the controllable curvature of the C-Au/4MBA@Ag NCs is directly modulated by adjusting the relative rates of the galvanic replacement and co-reduction reaction, which generates a controllable interparticle nanogap to offer large depositing spaces for analytes and improve authoritative SERS signals’ enhancement. The proposed C-Au/4MBA@Ag NCs exhibit an enhancement factor of up to 4.8 × 10 and contribute to the ultralow RSD (7.9%). These C-Au/4MBA@Ag NCs also enable the detection of hazardous pesticide residues such as methamidophos and thiram in herbal plants with a complex matrix, with an average detection accuracy of up to 96%. In summary, this study achieves a fine control strategy of the “crescent arc” surface for improving SERS performance and explores the practical application potential for accurate and sensitive Raman detection of hazardous substances.