Copper phthalocyanine (CuPc) and copper formazan (CuFz) are typical coordination compounds widely utilized due to their physicochemical properties and biochemical behavior. The production and application of CuPc and CuFz have produced large amounts of copper-containing wastewater and aromatic organics, posing great risks to human health and the environment. This research introduced a feasible and efficient treatment method based on BDD anodic oxidation for CuPc and CuFz wastewater and provided a novel perspective on the degradation differences of the two pollutants through DFT calculation. Firstly, the color removal efficiency and chemical oxygen demand (COD) during the anodic oxidation of the two molecules were compared. Secondly, the effect of pH, inorganic anions type, and current density on the oxidative degradation of CuPc and CuFz was discussed. Thirdly, cyclic voltammetry (CV) was carried out to evaluate the direct anodic oxidation speed of CuPc and CuFz. Then, the principal reactive oxygen species (ROS) of CuPc and CuFz in the indirect oxidation process were investigated through free radical quenching and Electron paramagnetic resonance (EPR) spectroscopy. The functional group changes in degradation, the degradation products, and the shed copper ions were also analyzed. Finally, the global, local, and condensed properties and CuPc and CuFz reaction sites to be attacked by ROS were theoretically analyzed using density functional theory (DFT) calculation. Altogether, this study can help broaden the discussion and further the understanding of the links between the electrochemical oxidation pathway and decolorization of coordination compounds.