Spinel lithium tianate Li4Ti5O12 (s-LTO) is attractive for its usage as the anode material in lithium-ion batteries due to its excellent cycling stability, but such an application is very often limited by its low electronic conductivity. This work demonstrates a new electron-probe nanofabrication approach to improving the electronic conductivity of spinel s-LTO. The conducting nano-channels through the s-LTO nanoparticles with the lateral dimension of ∼2nm are fabricated using a sub-nm electron probe in a scanning transmission electron microscope (STEM). These nano-channels consist of a single phase of Li4Ti5O12−x with a rocksalt structure (r-LTO). Using in-situ I–V measurements, we show a gradual increase of electronic conductivity of a single r-LTO nanoparticle up to 5 orders of magnitude of the original s-LTO phase under e-beam irradiation. The local structural analysis, through electron diffraction and high-resolution STEM imaging, reveals the lattice coherence between the induced r-LTO phase and s-LTO, with an orientation relationship of <110>r-LTO//<110>s-LTO and {111}r-LTO//{111}s-LTO. Moreover, under the electron irradiation, the O lattice retains, while all the tetrahedral-coordinated Li ions in the s-LTO migrate to the octahedral sites during the phase transformation. Our results suggest that the s-LTO/r-LTO nano-composite particles with enhanced electronic conductivity are an excellent candidate for the anode materials for lithium-ion batteries.