Spinel lithium titanate, Li4Ti5O12 (LTO) is attracting much attention as an alternative material replacing carbon based anodes in lithium ion batteries, due to its high rate properties as well as its durability and safety. The coexistence of the two phases, spinel Li4Ti5O12 and rock salt Li7Ti5O12, during the charge–discharge reactions is the key issue for the understanding of reaction mechanism and the development of LTO electrodes with improved performance. However, the two-phase distribution morphology in real LTO electrodes has not yet been reported, due to the difficulty in identifying the Li-inserted Li7Ti5O12 phase with high resolutions. Thus we apply the scanning transmission electron microscopy with electron energy loss spectroscopy (STEM–EELS) using the latest equipment with high energy and spatial resolutions. We have successfully identified the presence of the Li7Ti5O12 phase in Li-inserted LTO secondary particles, by the EELS analysis of Li composition, Ti oxidation state, and local configurations around oxygen atoms, compared to the Li4Ti5O12 phase. We have also obtained the two-phase distribution image in 50% Li-inserted LTO secondary particles, where separate presence of both the phases is clearly revealed. This indicates the particle-by-particle reaction mechanism, where the rate determining process exists in the boundary between primary particles.