Dissolved organic matter (DOM) is known to form strong complexes with heavy metals and thus governs the distribution, toxicity, bioavailability, and ultimate fate of heavy metals in the environment. The relevant aspects of metal-organic interactions remain unclear because the metal binding functionalities in DOM are substantially nonuniform and the availability of the models is limited. In this work, two-dimensional correlation spectroscopy (2DCOS) integrated with synchronous fluorescence and infrared absorption spectroscopy was used to explore the binding process of copper to DOM. A series of heterogeneous binding sites in humic acid (HA), a representative DOM, and the subsequent subtle changes of these sites within the molecular interactions were elucidated by the 2DCOS method. The band assignments and the correspondence between the results obtained by two spectral probes (synchronous fluorescence and infrared absorption spectra) were verified by hetero-2DCOS. Our results showed that, during the copper binding process, the carboxyl and polysaccharide groups gave the fastest responses to copper binding. Then fluorescence quenching of fluorescent humic-like moieties occurred with a vibrational change of the related functionalities, i.e., phenolic and aryl carboxylic groups, which further induces the fluorescence quenching of fulvic-like fractions. Finally, small amounts of amide and aliphatic groups participated in the copper binding after the fluorescence of the protein-like fraction decreased. With these promising results, a comprehensive picture of structural changes of HA during the copper binding process was developed, highlighting the superior potential of 2D heterospectral correlation spectroscopy in studying complex interactions in the environment.