An archetypical Li-rich layered oxide, Li2MnO3, shows a large initial charge capacity of ~350 mAh g-1 with little oxidation of the constituent Mn ions, yet, the crystal structure of delithiated Li2MnO3 is still unclarified because the structural disorder induced by the considerable Li extraction makes the analysis challenging. X-ray pair distribution function (PDF) analysis is a powerful tool to experimentally elucidate the structure of the disordered phase. Here, we conducted a comprehensive analysis with a focus on PDF analysis in combination with the X-ray powder diffraction (XRPD), transmission electron microscopy (TEM), and X-ray absorption spectroscopy (XAS) to reveal the disordered crystalline structure of the electrochemically delithiated Li2MnO3. The XRPD and TEM analyses clarified the formation of a low-crystallinity phase in the light of the average structure. The XAS and PDF analyses further revealed that the MnO6–based framework was rearranged with maintaining the MnO6 octahedral coordination after the initial charge. The difference pair distribution function (d-PDF) technique was therefore employed to extract the structural information of the low-crystallinity disordered phase. The delithiated phase was found to have a structure similar to the cubic spinel, LiMn2O4, rather than that of delithiated LiMn2O4 (λ-MnO2). In addition, the middle-range order of the delithiated phase deteriorated after the charge, indicating a decrease of coherent domain size to a single nm order. The composite structure formed after the first charge, therefore, consists of the disordered cubic spinel structure and unreacted Li2MnO3. The formation of the composite structure “activates” the electrode material structurally and eventually induces characteristic large capacity of this material