Ammonium ions (NH4+), as non-metallic charge carriers, have spurred great research interest in the realm of aqueous batteries. Unfortunately, most inorganic host materials used in these batteries are still limited by the sluggish diffusion kinetics. Here, we report a unique hydrogen bond chemistry to employ covalent organic frameworks (COFs) for NH4+ ion storage, which achieves a high capacity of 220.4 mAh g–1 at a current density of 0.5 A g–1. Combining the theoretical simulation and materials analysis, a universal mechanism for the reaction of nitrogen and oxygen bridged by hydrogen bonds is revealed. In addition, we explain the solvation behavior of NH4+, leading to a relationship between redox potential and desolvation energy barrier. This work provides a new insight into NH4+ ion storage in host materials based on hydrogen bond chemistry. This mechanism can be leveraged to design and develop COFs for electrochemical energy storage.