Co3O4 hollow nanospheres 15 nm in the diameter were assembled to the mesoporous polyhedron together with carbon. Within the Co3O4 polyhedrons, the bubbles 300–500 nm in diameter were uniformly generated. Every bubble further encapsulated one TiO2 nanosphere, forming a unique sphere-bubble structure. The specific surface area and the pore volume were calculated to be 97.85 and 0.31 cm3 g−1. When evaluated as anode material for lithium ion batteries, the as-prepared material exhibited superior lithium storage properties with high specific capacity, excellent cycling stability and good rate capability. After 400 cycles, the discharge capacity of 609 mAh g−1 was still delivered at current density of 335 mA g−1. Even at a high current density of 2000 mA g−1, the reversible capacity reached 296 mAh g−1. The outstanding electrochemical performance was attributed to the unique hybrid structure, which avoids nanomaterial aggregation, promotes ion diffusion and electron transfer, accommodates volume change of Co3O4 during (de)lithiation process, enhances structure strength, cycling stability and space utilization ratio of the hollow material.