Lithium ion batteries are the most feasible energy storage technology for modern society. However, the electrochemical performance of commercial products is not satisfactory, which severely limits the development of electrode materials. An urgent call to balance the demands of high surface area, rich site activity, enhanced electrical conductivity, and controlled electrochemical stability becomes even more desired. In this work, we report a Co3O4 hexagonal prism (CHP) with a unique anisotropy structure as the anode material for lithium ion storage. Specifically, the CHP has a solid microframework on the six sidewalls and porous nanotunnels on the top and bottom surfaces, which not only enhances lithium ion storage and transmission but also provides sufficient electrochemical stability (i.e., minimize volume expansion). Additionally, it has much higher Co3+ contents and oxygen vacancies on all the surfaces which contribute to rich site activity and enhanced electrical conductivity. Based on these, the anisotropy CHPs show a remarkably higher initial capacity, excellent rate capability, and unique cycling stability than those of Co3O4 nanowires and commercial Co3O4 microparticles. The resulting CHP electrodes demonstrate an excellent reversible capacity of 800 mA h g-1 after 800 cycles at 1 A g-1. A further mechanistic study reveals the relationship between the material properties and the electrochemical performances, which can be mainly attributed to the synergistic effect of the anisotropy architecture, the surface pseudocapacitance, and the enriched Co3+ on the material surface. This synthetic strategy provides insights for the development of high-performance anodes.