Graphite is widely used as a negative electrode material for lithium-ion batteries. Although it is well known lithium ions are inserted between the graphene layers, the details of the structural transition they undergo are not well understood. In this study, we performed operando structural analyses of graphite electrode during the discharge process using neutron diffraction and synchrotron radiation X-ray diffraction and established a solid foundation to clarify the relationship among the LiCx composition, discharging profile, and phase evolution of lithium-intercalated graphite (LIG). The operando analyses enabled us to assess simultaneously the structural changes of LIG along the ab plane (in-plane structure) and the c-axis direction (stage structure). In the de-lithiation process, the intralayer transition was observed on the ab plane from the LiC6-type to the LiC9-type arrangement near the LiC18 composition. The LiC9-type arrangement was retained in the Li-poorer phases such as LiC27, LiC36, LiC54, and LiC72, where the Li de-lithiation proceeded with the interlayer transition to higher-order stages. The phase transition of LIG involves a rapid switchover between the LiC6-type and the LiC9-type intralayer arrangement along with the changes in the interlayer stage structure. A reaction mechanism for the configurational transition on the intralayer and interlayer structure was updated.