To support a sustainable energy development, CO2 reduction for carbon neutralization and water-splitting for hydrogen economy are two feasible technical routes, both of which require a significant input of renewable energies. To efficiently store renewable energies, secondary batteries will be applied in great quantity, so that a considerable amount of energy needs to be invested to eliminate the waste battery electrolyte pollution caused by heavy metals including Cu2+, Zn2+ and Pb2+. To reduce this energy consumption, the removal behaviors of these ions by using clinoptilolite and zeolite A under 5, 7 and 10 BV h−1 in a fixed-bed reactor were investigated. The used zeolites were then regenerated by a novel NH4Cl solution soaking, coupled with the ultrasonication method. Further characterizations were carried out using scanning electron microscopy, N2 adsorption and desorption test, and wide-angle X-ray diffraction. The adsorption breakthrough curves revealed that the leaching preference of clinoptilolite was Pb2+ > Cu2+ > Zn2+, while the removal sequence for zeolite A was Zn2+ > Cu2+ > Pb2+. The maximum removal percentage of Zn2+ ions for clinoptilolite under 5 BV h−1 was 21.55%, while it was 83.45% for zeolite A. The leaching ability difference was also discussed combining with the characterization results. The fact that unit cell stayed the same before and after the regeneration treatment approved the efficacy of the regeneration method, which detached most of the ions while doing little change to both morphology and crystallinity of the zeolites. By evaluating the pH and conductivity changes, the leaching mechanisms by adsorption and ion exchange were further studied.