The divalent metal ion Cu²⁺ exceeds the standard in water sources and soils around many industrial and mining enterprises, causing deterioration of the ecological environment, and traditional chemical and biological treatments are prone to secondary pollution. Fulvic acid is composed of molecular clusters with similar properties. It has the characteristics of good water solubility, strong complexation and high chemical activity. It can efficiently control the distribution, migration and bioavailability of Cu²⁺ in the environment and is a hot spot in scientific research in recent years. Modern multispectral characterization analysis is helpful to reveal the changes in the structure-activity relationship between fulvic acid and metal ions, environmental effects and the migration behavior of heavy metal ions. It has important scientific value for studying the characteristics and mechanism of the complexation process of fulvic acid and Cu²⁺. This article reviews the basic theoretical research on the complexation of fulvic acid with Cu²⁺ in recent years. This paper further analyzes the characterization of fulvic acid and Cu²⁺ before and after complexation through infrared spectroscopy, fluorescence spectroscopy, differential spectroscopy, and interdisciplinary collaborative research. The effects of pH, ion concentration and the difference in composition of fulvic acid on the complexation process were discussed. The complex sites’ structural characteristics and action rules between fulvic acid and Cu²⁺ are revealed. Oxygen-containing acidic functional groups, such as carboxyl and phenolic hydroxyl, are the main complex sites between the complexation process of Cu²⁺ and fulvic acid. The carboxyl site has a significant ability to complex Cu²⁺. The phenolic hydroxyl site is helpful to increase the stability of the Cu²⁺and fulvic acid complex, and the nitrogen-containing functional group also plays an important role in the complex process. On this basis, this article further points out that the change of pH value will change the affinity of the active site of fulvic acid to Cu²⁺, the reason is mainly related to the ion exchange between Cu²⁺ and H⁺ on the active site and the electrostatic attraction of fulvic acid. The difference in FA components affects the complexation of FA and Cu²⁺, which is mainly reflected in the different numbers of phenolic hydroxyl, carboxyl and nitrogen-containing functional groups in different FA. The coexistence of Fe³⁺, Mg²⁺ and Al³⁺ the solution will have significant competition with Cu²⁺ at the active binding site of fulvic acid. At the same time, the concentration of non-strong adsorption ions such as K⁺ and Na⁺ in the solution environment increases, so that a large number of positively charged ions in the solution enter the electronic layer of fulvic acid nearby to enhance the charge shielding effect, inhibiting the complexation of Cu²⁺ and FA. Finally, this paper summarizes and looks forward to the problems and challenges of coexistence of scientific application of fulvic acid-related disciplines and technical theories in modern agriculture, ecological restoration and environmental governance.