Ion exchange is a promising synthetic method for alleviating severe cation mixing in traditional layered oxide materials for lithium-ion batteries, leading to enhanced structural stability. However, the underlying mechanisms of ion exchange are still not fully understood. Such a fundamental study of the ion-exchange mechanism is needed for achieving the controllable synthesis of layered oxides with a stable structure. Herein, we thoroughly unearth the underlying mechanism that triggers the ion exchange of Ni-rich materials in aqueous solutions by examining time-resolved structural evolution combined with theoretical calculations. Our results reveal that the reaction pathway of ion exchange can be divided into two steps: protonation and lithiation. The proton is the key to achieving charge balance in the ion exchange process, as revealed by X-ray adsorption spectroscopy and inductive coupled plasma analysis. In addition, the intermediate product shows high lattice distortion during ion exchange, but it ends up with a most stable product with high lattice energy. Such apparent discrepancies in lattice energy between materials before and after ion exchange emphasize the importance of synthetic design in structural stability. This work provides new insights into the ion-exchange synthesis of Ni-rich oxide materials, which advances the development of cathode materials for high-performance lithium-ion batteries.