For the intercalation type cathode in lithium-ion batteries, the structural framework of electrode is expected to remain unchanged during lithium insertion and extraction. Unfavorable phase transition in electrode materials, which has been frequently observed, modifies the structural framework, which leads to capacity loss and voltage decay. Here, we track atoms motion/shift in lithium manganese oxide during a phase transition from spinel to rocksalt by using atomically resolved aberration corrected scanning transmission electron microscopy and spectroscopy. We find that when given energy, the transition metal cation can readily hop between oxygen tetrahedral and octahedral sites in oxygen deficient lithium manganese oxide similar to lithium diffusion behavior, which leaves the anion structure framework almost unchanged. During this phase transition, the intermediate state, migration length, and atomic structure of phase boundaries are revealed, and the mechanism is discussed. Our observations help us to ...