We report on the delicate design and controllable preparation of Li4Ti5O12 (LTO) hollow micro-cubes by self-sacrificial template method and their application for lithium ion storage. The micro-nano structure of LTO hollow cube largely shortens the diffusion path of ion/electron, increases the contact surface and improves its structure stability. More importantly, the tailored Li4Ti5O12 hollow micro-cubes electrode shows an excellent rate performance and high capacity with a reversible capacity of 184, 123 and 80 mA h g−1 at current density of 1, 40 and 100 C, respectively. Meantime, a reversible capacity of 125 mA h g−1 is obtained after 5000 cycles at 20 C with a capacity retention of 92.5%, implying its superior stability. As anode for full batteries, matched with different cathodes (LiCoO2 or LiNi0.5Co0.5O2), it exhibits prominent stability, compatibility with high energy density of 363.0 and 326.1 Wh kg−1.