It is challenging to create cation vacancies in electrode materials for enhancing the performance of rechargeable lithium ion batteries (LIBs). Herein, we utilized a strong alkaline etching method to successfully create Co vacancies at the interface of atomically thin Co3−xO4/graphene@CNT heterostructure for high-energy/power lithium storage. The creation of Co-vacancies in the sample was confirmed by high-resolution scanning transmission electron microscope (HRSTEM), X-ray photoelectron spectroscopy (XPS) and electron energy loss near-edge structures (ELNES). The obtained Co3−xO4/graphene@CNT delivers an ultra-high capacity of 1688.2 mAh g−1 at 0.2 C, excellent rate capability of 83.7% capacity retention at 1 C, and an ultralong life up to 1500 cycles with a reversible capacity of 1066.3 mAh g−1. Reaction kinetic study suggests a significant contribution from pseudocapacitive storage induced by the Co-vacancies at the Co3−xO4/graphene@CNT interface. Density functional theory confirms that the Co-vacancies could dramatically enhance the Li adsorption and provide an additional pathway with a lower energy barrier for Li diffusion, which results in an intercalation pseudocapacitive behavior and high-capacity/rate energy storage.