Understanding carboxyl-metal ligand interaction has great significance in analytical chemistry. Herein, we use resonant surface-enhanced Raman scattering (SERS) to probe the physiochemical interaction and conformation change in several metal ion-carboxyl coordination complex systems adsorbed on the surface of plasmonically resonant metal nanostructures. Our SERS results and density function theory calculations jointly reveal that low-valence metal ions (such as K+ and Pb2+) tend to bind to the carboxyl active site of a Raman tag molecule, 4-mercaptobenzoic acid (4-MBA), in a unidentate binding mode of low binding energy whereas high-valence metal ions (such as Fe3+) favor a bidentate binding mode of relatively high binding energy. Particularly, Pb2+-ion concentration-dependent SERS suggests a repulsive interaction among the coordination complex leading to a tilted configuration of 4-MBA on the metal surface. This work indicates the resonant SERS approach is suitable not only for studying the carboxyl-metal ligand interaction but also for detecting various types of heavy metal ions at low concentrations.