TiO2 nanocrystals in rutile, anatase and mixed phase were prepared from the titanium iso-propoxide precursor by employing a controlled amount of HCl as a peptizing agent along with the hydrothermal treatment without any surfactants at 100°C, 150°C and 200°C for 10h. The as obtained nanocrystals at 150°C (NP150) is found to be shorter nanorods with an average diameter of ~12nm and length of ~32nm showing a typical anatase characteristics with 2θ peak positions at 25.27°, 37.80°, 48.09°, 54.02°, 54.77°, 62.80°, 69.16° and 70.17°. However, the 100°C and 200°C samples with same reaction protocol produces only aggregated nanoparticles with a rutile and a mixed anatase/rutile crystal phases, respectively. The as obtained shorter nanorod structures when processed for the electrochemical test as anode materials in lithium ion battery shows an excellent first and second discharge capacities of 366 and 182mAhg−1 with a plateau of 1.72V, much higher than those of nanoparticle (100°C and 200°C). The enhanced capacity could be attributed to the defect free, anatase crystal phase, stable morphology, high surface area and an enhanced conductivity due to the nanorods morphology which could effectively withstand expansion/contraction occurring during the successive lithium ion insertion/extraction process.