An anion-exchange-based chromatographic separation approach was developed to selectively recover zinc and copper from the high-chlorine raffinate generated in the process of germanium chlorination distillation using 717 resins based on the coordination difference between Zn²⁺/Cu²⁺ and Cl^-. The theoretical calculation and spectroscopic analyses suggested that the coordination between Zn²⁺ and Cl^- is much stronger than that between Cu²⁺ and Cl^-, and the Cl^- concentration significantly affects Zn(II) and Cu(II) species. The factors involving Cl^- concentration, resin dosage, shaking speed, and temperature were investigated to determine the optimal condition, and the maximum separation factor of Zn/Cu reached as high as 479.2. The results of the adsorption isotherms, adsorption kinetics, SEM, FTIR, and XPS analyses indicated that the process followed the monolayer uniform chemisorption. Through the continuous adsorption experiments, Zn(II) and Cu(II) in the high-chlorine raffinate were separately recovered, allowing the reuse of residual waste acid and germanium.