Density functional and two-layer ONIOM methods were used to understand the interactions of various ion-exchanged zeolites with one and multiple H2 molecules. It indicates that dispersion interactions among H2 molecules and local exchanged sites rather than from zeolite lattices play a significant role. At most two H2 molecules can be chemisorbed on the MIIIO species. The H2 reduction energy barriers increase with more chemisorbed H2 molecules or by formation of H-bonds with the extra-lattice O atom until covered up. For metal ions of identical valence state, Lewis acidity decreases with radius increase, causing larger adsorption capacity but smaller adsorption strength. For metal ions of close radii, Lewis acidity increases with valence state, corresponding to larger adsorption strength and capacity. The Lewis acidity of each metal ion within zeolites gradually decreases with H2 loading, but the adsorption energies do not change monotonously with H2 loading, probably due to that the H atoms usually show positive charges as metal ions and thus behave different from other molecules. The apparent H2 adsorption energies and capacities are determined for all the studied metal ions. It is testified that that the LaIII ion is a good candidate for hydrogen storage that six H2 molecules can be chemisorbed. The La ion tends to interact with H2 via the end-on mode and differs from others where the side-on mode is preferred. This work offers a systematic study of hydrogen adsorption on metal ions within zeolites and helps to design zeolite-based or other materials for hydrogen storage.