Exploration of high‐performance aqueous ammonium‐ions hybrid supercapacitor has attracted tremendous research attention recently. Herein, structural reconstructed cobalt‐iron layered double hydroxides (SR‐CoFe LDHs) featuring copious structure defects (i. e., oxygen‐vacancies, M−O bonds, MOO− bonds, coexistence of Co2+/Co3+ and Fe2+/Fe3+) are reported as a high‐capacity cathode for NH4+ storage. The resulting SR‐CoFe LDHs can deliver a reversible capacity of 167.9 mAh g−1 at 0.5 A g−1, which is 3.3 folds higher than that of pristine CoFe‐LDHs. Ex‐situ experimental results and theoretical studies denote that the presence of structural defects in the CoFe‐LDHs can lower the NH4+ adsorption energy and induced electron delocalization to enhance the electrical conductivity, rendering the CoFe‐LDHs exhibits excellent performance for NH4+ storage. As a proof of concept, ammonium‐ion hybrid supercapacitor has been assembled with CoFe‐LDHs as the cathode and hierarchical carbon as the anode, which can deliver a large specific capacitance of 238.3 F g−1, long cycle stability over 10000 cycles, and high energy density of 66.2 Wh kg−1 within a wide working voltage of 2 V. Overall, this work offers some insights into the design of high capacity cathode for aqueous NH4+ storage and also illustrates the construction of aqueous hybrid devices with NH4+ as the charge carrier.