Flower-like hydrogenated TiO2(B) nanostructures have been synthesized via a facile solvothermal approach combined with hydrogenation treatment. The obtained TiO2(B) nanostructures show uniform and hierarchical flower-like morphology with a diameter of 124 ± 5 nm, which are further constructed by primary nanosheets with a thickness of 10 ± 1.2 nm. The Ti3+ species and/or oxygen vacancies are well introduced into the structures of TiO2(B) after hydrogen reduction, resulting in an enhancement in the electronic conductivity (up to 2.79 × 10−3 S cm−1) and the modified surface electrochemical activity. When evaluated for lithium storage capacity, the hydrogenated TiO2(B) nanostructures exhibit enhanced electrochemical energy storage performances compared to the pristine TiO2(B) nanostructures, including high capacity (292.3 mA h g−1 at 0.5C), excellent rate capability (179.6 mA h g−1 at 10C), and good cyclic stability (98.4% capacity retention after 200 cycles at 10C). The reasons for these improvements are explored in terms of the increased electronic conductivity and the facilitation of lithium ion transport arising from the introduction of oxygen vacancies and the unique flower-like morphologies.