Anatase TiO₂ is a promising anode material for lithium-ion batteries (LIBs) owing to its low cost and stability. However, the intrinsically kinetic limits seriously hindered its lithium-ion storage capability. Here we present that anatase TiO₂ with rich oxygen vacancies can enhance its lithium-ion storage performance. We synthesize anatase TiO₂ with well-retained hierarchical structure by annealing the H₂Ti₅O₁₁·3H₂O yolk-shell spheres precursor in nitrogen atmosphere. EPR and XPS data evidence that the oxygen-deficient environment could generate abundant oxygen vacancies in the as-derived anatase TiO₂, which leads to improved electron conductivity and reduced charge-transfer resistance. The rich oxygen vacancies and high structural integrity of the hierarchical yolk-shell spheres enable the as-derived anatase TiO₂ yolk-shell spheres with a high specific capacity of 280 mAh g⁻¹ at 100 mA g⁻¹ and 71% of capacity retention after 5000 cycles at 2 A g⁻¹.