The Co3O4 as anode for lithium ion batteries (LIBs) suffers the sluggish electrode kinetics and severe capacity fade during the cycles. The defective engineering of Co3O4 with oxygen/cobalt defects is an effective strategy to optimize Co3O4 with enhanced electrochemical properties. Herein, a series of 3D inter-connected Co3-xO4@C-y nanostructures with abundant Co defects are synthesized through a hydrothermal approach with subsequent heating-controlled process. Benefiting from its rich surface cobalt-defective sites and the 3D interconnected frameworks, as well as its high surface area and residual carbon layer, the Co3-xO4@C-y synthesized at y = 400 °C as anode for LIBs displays superior pseudocapacitive lithium storage properties with an ultra-high reversible specific capacity of 1900.7 mAh g−1 at 0.2 A g−1, excellent rate capability (e.g., 1415.1 mAh g−1 at 10 A g−1) and ultra-long cycling stability (e.g., 1160.5 mAh g−1 at 15 A g−1 after 2000 cycles).