For more than five decades, dithizone has been widely used as an analytical reagent. This ligand forms strongly colored complexes with metal ions and this ability to form complexes can be used for extraction/removal of certain metal ions in addition to analytical determination. In static mode, the supercritical carbon dioxide extraction of copper and lead ions from aqueous solutions after complexation by the dithizone ligand is studied (at two different conditions: a) p = 120 bar, T = 30 °C, and b) p = 72 bar, T = 50 °C). The addition of methanol improved the extraction process by modulating the polarity of the extraction medium. Atomic absorption spectroscopy (AAS) is used to determine the concentration of metal ions before and after extraction. We use density functional theory (DFT) [model chemistry: using m-GGA/M11-L] to better understand the binding energy and geometry of bidentate ligands produced from dithizone and copper(II) or lead(II) ions. Furthermore, the developed complexes' noncovalent interactions (NCI), bond order analysis, and electron localization function (ELF) provided valuable details about these molecules. To elucidate the bidentate complex extraction mechanism formed between the heavy metal ions and the dithizone ligand, molecular dynamic simulations at periodical boundary conditions were performed using the universal force field to obtain precise molecular descriptions.