Honeycomb-layered phases like Na3Ni2SbO6 have been extensively researched as high-voltage and high-rate capability cathode materials for sodium-ion batteries. However, our understanding of the structural stability and dynamic reaction mechanisms of Na3Ni2SbO6 cathode during cycling, especially at atomic-scale, remains limited. Here, we track the microstructure evolution during extraction of Na+ ions in Na3Ni2SbO6 cathode at atomic scale in an aberration-corrected transmission electron microscope. The electron beam irradiation that can provide a driving force for the Na+ ion migration, allows us to mimic the battery charge process. By controlling the electron beam dose, we study the structure evolution behavior to obtain insights into understanding the work principle and failure mechanism of Na3Ni2SbO6 cathode under different charge rate conditions. We find that the real-time structural evolution and ion migration pathways of Na3Ni2SbO6 cathode are distinct under different electron beam doses. High-dose irradiation reveals Na ion depletion, surface cracks, and phase transformations, mimicking rapid capacity decay. In contrast, low-dose irradiation shows slower ion migration, ordered Na vacancy formation, and maintaining structural integrity, which more closely resembles the electrochemical process of actual battery. This study provides an atomistic understanding of the structural stability and Na ions deintercalation mechanism in Na3Ni2SbO6 cathodes, offering new insights into optimizing electrode materials.