Strong acidic heavy metal ions (HMIs) wastewater (pH < 3.0) is characterized by widespread source, mixed composition and high toxicity, which is extremely difficult to control and meet the requirements of HMIs separation and resource recovery. Herein, a novel aminophosphonic acid-functionalized hydrogel (CMC/PEI-P) was prepared successfully and applied to highly-selective separate Cu(II) from strong acidic media (SAM) (pH = 2.0). Thanks to the abundant and outward amino phosphonic acid groups, the maximum adsorption capacity and the initial adsorption rate constant were 119.41% and 116.64% higher than those of the precursor CMC/PEI. Most importantly, the exclusive separation with the super-high selectivity coefficients (+∞) could unexpectedly achieve with CMC/PEI-P even from the mixed polymetallic SAM. Furthermore, the purity of Co(II) in strong acidic cobalt-rich solution could be increased to more than 99.50%, with the benefit of about 200 times higher than the cost. The predominant mechanisms existed in the coordination with various active groups such as phosphonate, amine and hydroxyl. According to Density Functional Theory (DFT) calculations, the tetradentate coordination configuration with the best stability could be formed involving CMC/PEI-P and Cu(II). Therefore, this work explored a new pathway for the cost-effective separation and purification toward Cu(II) directly especially from SAM.