Emerging aqueous ammonium-ion batteries (AIBs) are considered inexpensive, highly safe, ecofriendly, and sustainable energy storage systems. Although some high-performance electrode materials have been reported for AIBs, a comprehensive understanding of the origin of the high ammonium-ion storage performance is still lacking. Herein, the percolating network of anionic vacancies is determined to be the origin of the superior ammonium-ion storage properties of the Prussian blue analogues based on ab initio molecular dynamics simulation and electrochemical kinetic analyses. Fe[Fe(CN)6] with a percolating anionic vacancy network delivers an outstanding rate of 64.7 mAh g-1 at 2000 mA g-1 in addition to a capacity retention of 94.5% after 10 000 cycles. The low-strain intercalation ammonium-ion storage mechanism of highly deficient Fe Prussian blue with Fe as the redox center is revealed by in situ X-ray diffraction and ex situ X-ray absorption fine structure analysis. The results provide insights into the mechanism of ammonium-ion storage in Prussian blue analogues and guidance in the development of aqueous AIBs.