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Selective ion-exchange with zeolites has been considered as one of the most promising means to remove a radioactive isotope of cesium, 137Cs, present in low concentration in seawater. However, there has been no report on the fundamental structure–property relation of zeolite-based Cs ion-exchangers. In this study, we investigate the origin of the selectivity of the radioactive cesium isotope in zeolite frameworks using zeolite A (LTA) as a model system. We prepared seven single crystals of fully dehydrated and partially cesium exchanged Zeolite A (LTA) with different Cs+/Na+ ratios. Their single-crystal synchrotron X-ray diffraction experiments revealed the significant differences in the degree of exchange and the site selectivity of Cs+ ions depending on the initial Cs+ concentrations in given ion exchange solutions. The degree of Cs+-ion exchange increases from 15.8 to 44.2% as the initial Cs+ concentration increases and the Na+ content decreases. In addition, it was found that Cs+ ions are energetically preferred and occluded in the center of eight-oxygen rings. With this finding, we tested the Cs adsorption capacity of pure zeolite Rho which has much more eight-oxygen rings than zeolite A along with commercial faujasite-type zeolite and titanosilicate from deionized water and seawater. Zeolite Rho showed significantly better performance on the Cs removal in the presence of high salt contents (i.e., seawater) than faujasite-type zeolite and titanosilicate.