TiO2 nanoparticles containing oxygen vacancies mostly existed in the bulk phase, and the counterpart with oxygen vacancies both on the surface and in the bulk phase, were successfully prepared via calcination of nanotube titanic acid under air and H2 atmosphere respectively. The effect of surface and/or bulk oxygen vacancies on the structure and electrochemical properties of electrode materials were studied. The materials characterization results demonstrate that under air atmosphere, the obtained TiO2 nanoparticles containing oxygen vacancies mainly in the bulk phase, while its surface still remains the stoichiometric structure. While hydrogenation process leads to a crystalline-disordered core–shell structure, oxygen vacancies existed both on the surface and in the bulk of TiO2 nanoparticles. As-fabricated TiO2 samples containing oxygen vacancies exhibit markedly improved electrochemical properties comparison with TiO2 nanoparticles without defects. Oxygen vacancies can act as physical space for Li-ion storage thus improve the specific capacity of electrode, the enhanced rate performance mainly origin from the bulk oxygen vacancies.