The improvement of fast-charging capabilities for lithium-ion batteries significantly influences the widespread application of electric vehicles. Fast-charging performance depends not only on materials but also on the battery’s inherent structure and the heterogeneity of the electrode reaction. Herein, we utilized advanced imaging techniques to explore how the internal structure of cylindrical batteries impacts macroscopic electrochemical performance. Our research unveiled the natural 3D structural non-uniformity of the electrodes, causing heterogeneity of electrode reaction. This non-uniformity of reaction exhibited a macro–meso–micro-scale feature in four dimensions: the exterior versus the interior of the electrode, the middle versus the sides of the cell, the inside versus the outside of the cell, and the surface versus the body of the electrode. Furthermore, the single-coated side of the anode demonstrated notably faster reaction than the double-coated sides, leading to the deposition of island-like lithium during fast charging. These discoveries offer novel insights into multi-scale fast-charging mechanisms for commercial batteries, inspiring innovative approaches to battery design.