Owing to the high spatial resolution at the atomic scale, the transmission electron microscopy (TEM) or scanning transmission electron microscopy is demonstrated as a promising characterization method to unveil the charge storage mechanism of electrode materials in Li-ion batteries. The structural evolution of electrode materials during charge/discharge process can be directly observed by using TEM. The detailed analysis establishes a relationship between the structure of electrode material and battery performance. Herein, we present a brief review of the atomic-scale characterization in Li-ion batteries, including Li (de)insertion mechanism (both cations and anions charge-compensation mechanism), migration of transition metal ions, and surface phase transition. The in-depth microscopic analysis reveals the detailed structural characteristics, which influence the properties of LIBs, establish the structure–function relationship, and facilitate the development of Li-ion batteries.