Owing to unique textural morphologies and definite shorter ionic diffusion paths through nano size pore walls, ordered mesoporous materials have received great attention in energy storage applications. Herein, we report synthesis of ordered mesoporous Co3O4 via uni-directional hexagonal MCM-41 and three dimensional cubic MCM-48 silica templates. The products derived from MCM-41 and MCM-48 designated as M1-Co3O4 and M8-Co3O4 which exhibit nanowire (1D) and honeycomb (3D) morphologies respectively. Further, the materials were evaluated for electrochemical lithium ion storage applications as anodes. Both the mesoporous Co3O4 materials show high initial reversible capacities (75% coulombic efficiency), excellent electrochemical cycling stability and enhanced rate performance. For example, at 1C rate M1-Co3O4 delivers discharge capacity of 1190 mA h g−1 and M8-Co3O4 exhibits 790 mA h g−1 after 100 charge–discharge cycles. Similarly, at 10C after 1000 cycles M8-Co3O4 shows 570 mA h g−1 whereas M1–Co3O4 delivers discharge capacity of ∼500 mA h g−1. Further, electrochemical impedance studies and post-mortem HRTEM analyses support the enhanced electrochemical long-term cycling stability and excellent structural stability. Hence, we believe Co3O4 with ordered mesoporous structure can be potential candidate as anode for lithium ion battery applications.