The aqueous ammonium ion (NH4+) is a promising charge carrier in virtue of its safety, environmental friendliness, abundant resources and small hydrated ionic size. The exploration of NH4+ host electrodes with good reversibility and large storage capacity to construct high-performance ammonium-ion hybrid capacitors (AIHCs), however, is still in its infancy. Herein, a facile etching technique is put forward to produce oxygen-deficient MnO2 (O-d-MnO2) as the electrode material for NH4+ storage. According to the experimental and theoretical calculation results, the etching process not only creates more porosity, offering abundant active sites, but also generates abundant oxygen vacancies, which modify the structure of pristine MnO2, enhance charge storage capacity and boost ion diffusion kinetics. Consequently, O-d-MnO2 can deliver a specific capacity of 155 mAh<middle dot>g(-1) at 0.5 A<middle dot>g(-1) and a good long-term cycling stability with 86.8% capacity maintained after 10,000 cycles at 5.0 A<middle dot>g(-1). Additionally, the NH4+ storage mechanism was evidenced by several ex-situ characterization analyses. To examine the actual implementation of O-d-MnO2 as a positive electrode for NH4+ full device, AIHCs are assembled with activated carbon functionalized with Fe3O4 nanoparticles (Fe3O4@AC) as a negative electrode. A high specific capacitance of 184 F<middle dot>g(-1) at 0.5 A<middle dot>g(-1), satisfactory energy density of 102 Wh<middle dot>kg(-1) at 500 W<middle dot>kg(-1), a low self-discharge rate and good cycling durability after 10,000 cycles are attained. The electrochemical performance of these AIHCs is comparable to or surpass those of traditional supercapacitors with metal ions as charge carriers, highlighting the advantages of structural modification in enhancing the NH4+ storage performance.