Surface-enhanced Raman scattering (SERS) has been widely used for bioanalysis because it provides a high sensitivity for detecting analytes of ultralow concentrations. However, the clinical application of a 2D SERS-active substrate remains challenging because of the difficulty of obtaining accurate quantification, especially at low concentration. In this study, we proposed an analytical method that integrates an optimized sample mapping strategy with an electrochemical SERS (EC-SERS) technique to resolve this problem. We adopted this method to detect two metabolites of azathioprine, namely 6-thioguanine nucleotides (6-TGNs) and 6-methylmercaptopurine (6-MMP), as our proof-of-concept experiment. We first prepared a conductive SERS-active substrate by electrochemically depositing Au nanoparticles (AuNPs) on indium tin oxide glass. The two metabolites were then randomly absorbed on the surface of the AuNPs of the SERS-active substrates. When we applied a negative potential on the substrate, we observed a large enhancement of Raman intensity for both metabolites, which was attributed to both the charge transfer effect and reorientation of metabolites on the substrate surface, leading to the formation of Au-S bonds. In addition, by optimizing the mapping range, we were able to efficiently reduce the standard deviation of SERS intensity and achieve a consistent standard deviation lower than 10%. With these two features, we were able to achieve quantitative analysis of 6-TGNs and 6-MMP with a detection limit of 10 and 100 nM, respectively. The integration of EC-SERS and the mapping method provided a reliable and quantitative analytical platform for analytes, which can be electrochemically modulated, like 6-TGNs and 6-MMP.