© 2020 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim Lithium-rich layered oxides are promising candidate cathode materials for the Li-ion batteries with energy densities above 300 Wh kg−1. However, issues such as the voltage hysteresis and decay hinder their commercial applications. Due to the entanglement of the transition metal (TM) migration and the anionic redox upon lithium extraction at high potentials, it is difficult to recognize the origin of these issues in conventional Li-rich layered oxides. Herein, Li2MoO3 is chosen since prototype material to uncover the reason for the voltage hysteresis as the TM migration and anionic redox can be eliminated below 3.6 V versus Li+/Li in this material. On the basis of comprehensive investigations by neutron powder diffraction, scanning transmission electron microscopy, synchrotron X-ray absorption spectroscopy, and density functional theory calculations, it is clarified that the ordering–disordering transformation of the Mo3O13 clusters induced by the intralayer Mo migration is responsible for the voltage hysteresis in the first cycle; the hysteresis can take place even without the anionic redox or the interlayer Mo migration. A similar suggestion is drawn for its iso-structured Li2RuO3 (C2/c). These findings are useful for understanding of the voltage hysteresis in other complicated Li-rich layered oxides.