Various interferences from measurement conditions and substrate inhomogeneity are well-known confounding factors for poor reproducibility, which is a challenge in surface-enhanced Raman scattering (SERS) quantification. To address these issues, novel substrates and versatile internal standards have been designed and the repeatability is improved to some degree. However, these internal standards are either complex or unstable enough to resist harsh environments such as acid and oxidation. Graphene-isolated-Au-nanocrystal (GIAN) has unique properties and been applied for cell multimodal imaging and chemotherapy but not for SERS quantification analysis yet. Herein, we chose GIANs to improve the accuracy of SERS analysis. GIAN integrates the SERS effect and internal standard into a simple nanoparticle and is proved to be an ideal platform for SERS analysis given its superior properties: (1) chemical stability, it remains stable in strong acid and oxidation, even mimic bioenvironment; (2) a simple core-shell structure, with a thin graphitic shell which is not only a protector that avoiding inner Au catalysis unnecessary reaction but also an internal standard to eliminate the interference during the Raman detections; (3) the big-Π structure can absorb target molecule thus achieve an enrichment effect and quench background fluorescence. Laser power, focus, and substrate fluctuations as well as coexist substance interferences were investigated and the accuracy was improved greatly with the introduction of 2D band internal standard in Raman silent region with less background. Moreover, GIAN was applied for crystal violet determination directly on fish muscle and scale, which was rapid and convenient without complex extraction process. All these results indicate GIAN is an optimum choice for SERS analysis in complex systems.