We report the development of a surface-enhanced Raman scattering (SERS)-based heavy metal ion sensor targeting the detection of mercury(II) ion (Hg(2+)) and copper(II) ion (Cu(2+)) with high sensitivity and selectivity. To achieve the detection of vibrational-spectroscopically silent heavy metal ions, the SERS substrate composed of gold nanorod (AuNR)-polycaprolactone (PCL) nanocomposite fibers was first functionalized using metal ion-binding ligands. Specifically, 2,5-dimercapto-1,3,4-thiadiazole dimer (di-DMT) and trimercaptotriazine (TMT) were attached to the SERS substrates serving as bridging molecules to capture Hg(2+) and Cu(2+), respectively, from solution. Upon heavy metal ion coordination, changes in the vibrational spectra of the bridging molecules, including variations in the peak-intensity ratios and peak shifts were observed and taken as indicators of the capture of the target ions. With rigorous spectral analysis, the coordination mechanism between the heavy metal ion and the corresponding bridging molecule was investigated. Mercury(II) ion primarily interacts with di-DMT through the cleavage of the disulfide bond, whereas Cu(2+) preferentially interacts with the heterocyclic N atoms in TMT. The specificity of the coordination chemistry provided both di-DMT and TMT with excellent selectivity for the detection of Hg(2+) and Cu(2+) in the presence of other interfering metal ion species. In addition, quantitative analysis of the concentration of the heavy metal ions was achieved through the construction of internal calibration curves using the peak-intensity ratios of 287/387 cm(-1) for Hg(2+) and 1234/973 cm(-1) for Cu(2+).