Various kinds of nanostructured materials have been extensively investigated as lithium ion battery electrode materials derived from their numerous advantageous features including enhanced energy and power density and cyclability. However, little is known about the microscopic origin of how nanostructures can enhance lithium storage performance. Herein, we identify the microscopic origin of enhanced lithium storage in anatase TiO2 nanostructure and report a reversible and stable route to achieve enhanced lithium storage capacity in anatase TiO2. We designed hollow anatase TiO2 nanostructures composed of interconnected ∼5 nm sized nanocrystals, which can individually reach the theoretical lithium storage limit and maintain a stable capacity during prolonged cycling (i.e., 330 mAh g–1 for the initial cycle and 228 mAh g–1 for the 100th cycle, at 0.1 A g–1). In situ characterization by X-ray diffraction and X-ray absorption spectroscopy shows that enhanced lithium storage into the anatase TiO2 nanocrystal results from the insertion reaction, which expands the crystal lattice during the sequential phase transition (anatase TiO2 → Li0.55TiO2 → LiTiO2). In addition to the pseudocapacitive charge storage of nanostructures, our approach extends the utilization of nanostructured TiO2 for significantly stabilizing excess lithium storage in crystal structures for long-term cycling, which can be readily applied to other lithium storage materials.