Zeolites are widely used for capturing radioactive Cs+ and Sr2+, but the important structural factors determining their performance have not been clearly understood. To investigate the structure-property relationship, we prepared thirteen zeolites with various structures and Si/Al ratios. Ion-exchange experiments revealed that Cs+ exhibited an enhanced affinity to zeolites with high Si/Al ratios, which could be explained by the dielectric theory. Notably, zeolites containing 8-membered ring (8MR) showed extra-high Cs+ selectivity. Structural analysis using X-ray diffraction proved that Cs+ with an ionic diameter of 3.6 Å was selectively coordinated within 8MR having a cavity diameter of 3.6–4.1 Å. Such unique size-selective Cs+ coordination is analogous to ion complexation by macrocyclic organic ligands (e.g., crown ethers). Divalent Sr2+ showed decreasing affinity to zeolites as the Si/Al ratio increased, because of the increasing average Al–Al distance distribution. Sr2+ exchange exhibited an insignificant dependence on zeolite structures due to its strong hydration, which inhibited close interaction with zeolite frameworks. In terms of kinetics, Sr2+ exchange was significantly slower than Cs+ exchange because of the bulkiness of hydrated Sr2+ ions. Therefore, the micropore channels with large apertures (e.g., 12-membered ring) were beneficial for achieving fast ion-exchange kinetics, especially in the case of Sr2+.