Humic acid is regarded as an eco-friendly material to manage heavy metal contamination due to its favorable binding characteristics to heavy metals. The heavy metal–humic acid ligand binding characteristics are critical for managing the migration and toxicity of heavy metals. We utilized parallel factor analysis (PARAFAC) to isolate humic acid compounds into individual ligands. Furthermore, the modified Stern–Volmer equation and the hetero-two-dimensional correlation spectroscopy (2DCOS) were used to elucidate the complexing characteristics of humic acid with Cd2+ and Cu2+, and good complexation properties between the ligands and heavy metals were observed. In the humic acid ligand, Cd2+/Cu2+ binding processes, the Cd2+ binding capability was significantly higher than for Cu2+. The binding rates of Cd2+ and Cu2+ and the humic acid ligands were negatively correlated with each other. The Cu2+/Cd2+ binding capacities of the humic acid ligands were associated with the humification degree of the humic acid compounds. Therefore, different humification degree humic acid compounds could separately employed to treat different heavy metal contaminations precisely and effectively. The humic acid ligand–heavy metal complexing characteristics were illustrated theoretically for the control of heavy metals in the environment. Therefore, this study provides a strategy for the recovery of waste resources from contaminated soils into useful products.