Li-rich layered oxides are promising as next-generation cathode materials for Li-ion batteries because of their potential to provide high voltage and large capacities. However, these materials suffer from significant voltage hysteresis between charge and discharge, and the causes are not yet well understood. In this work, a comprehensive in-situ X-ray diffraction analysis, conducted in Li2RuO3 as a model of Li-rich cathode materials, reveals that a discrepancy in the intermediate crystal phases formed during Li extraction and re-insertion gives rise to different electrochemical potentials between charge and discharge, which causes the undesired voltage hysteresis. These findings enrich the understanding of voltage hysteresis in Li-rich materials.