In layered materials, the layer-stacking sequence allows the tuning of ion transport and storage properties by modulating the host-ion interactions. However, unlike in the case of cations, the relationship between the stacking sequence and anion transport and storage properties is less clearly understood. Herein, we demonstrate that the stacking sequence governs the nitrate-storage properties of layered double hydroxides (LDHs); the 2H1 polytype enhances the nitrate-storage capacity to 400% of that of the 3R1 polytype. A quartz crystal microbalance with dissipation monitoring combined with multimodal ex situ experiments indicated that the high ion-storage capacity of the 2H1 polytype originates from the soft nature of LDHs lattices, which facilitates nitrate with minimal lattice changes. In contrast, the rigid lattice of the 3R1 sequence requires a notably large lattice expansion, which is detrimental to ion storage. Our findings can aid the rational design of anion-host interaction-derived functionalities.