A novel nanocomposite of crystalline Li4Ti5O12-coated TiO2 nanotube arrays (Li4Ti5O12/TNTA) was synthesized by anodic oxidation and sol-gel method as three-dimensional (3D) anode for Li-ion batteries. The 3D nanotubular structure was well retained in Li4Ti5O12/TNTA, and the pure and nanocrystalline Li4Ti5O12 formed on the surface of TNTA by the simple, template-free and low-temperature process. The morphology and microstructure of the samples were investigated by glancing angle X-ray diffraction (GAXRD), field emission scanning electron microscopy (FESEM), and transmission electron microscopy (TEM). In addition, the electrochemical performance was further evaluated by charge-discharge measurements and electrochemical impedance spectroscopy (EIS), and the formation mechanism of nanocrystalline of Li4Ti5O12 was discussed. The results showed that the new phase Li4Ti5O12 separated the phases of anatase and rutile, and hindered the phase transformation of anatase to rutile severely due to the steric hindrance effect, moreover nanocrystalline Li4Ti5O12 coating bonded TNTA firmly and improved the stability of the porous tubular structure. Li4Ti5O12/TNTA anode with the novel nanostructure exhibited higher electrochemical performance than that of TNTA. The areal capacity of Li4Ti5O12/TNTA anode is 400.9μAhcm−2 at the current density of 10μAcm−2, after 50 cycles of different current density it retains 175.8μAhcm−2, which is almost tripled of TNTA 63.9μAhcm−2.