Sodium hexatitanates (Na2Ti6O13) with tunnelled structures have been experimentally proposed to be good candidates for anode materials of lithium ion batteries because of their low potential, small shape transformation, and good reversibility. The understanding of the properties of this lithiated titanate is significant for their development. To this end, the first-principle calculations were performed to investigate the interaction between Li ions and Na2Ti6O13 at the atomic level. After structural optimization with various Li:Ti ratios, the Li ions are found to energetically prefer to stay at the small rhombic tunnels of Na2Ti6O13, where the diffusion energy barrier of Li ions is also lower. Such preference is determined by the chemical environment around Li ions. Our theoretical intercalation potential and volume change on the basis of the optimized atomic structures agree with the experimental observations. The analysis of the electronic properties reveals the Burstein-Moss effect in lithiated Na2Ti6O13 due to the heavy n-type doping. Such materials possess high conductivity, which can benefit their applications in photoelectrochemical or electrochemical areas.