A self-assembled Manganese (Mn) based metal organic complex (Mn-MOC) with spherical structure was synthesized via a solvothermal reaction. The Mn-MOC precursor materials were converted to hierarchical porous Mn3O4/C nanospheres through thermal annealing treatment. These nanospheres exhibited a high reversible specific capacity (1237 mAh/g at 200 mA/g), excellent ratability (425 mAh/g at 4 A/g), and extremely long cycle life (no significant capacity fading after 3000 cycles at 4A/g) as an anode in lithium ion batteries. The notable capability for lithium storage is attributed to the unique porous hierarchical structure of the Mn3O4/C nanospheres, which consist of homogeneously distributed Mn3O4 nanocrystals with thin carbon shells. Such a desired nanostructure not only provided large reaction surface area and enhanced electrical conductivity, but also promoted the formation of a stable solid electrolyte interphase (SEI) and accommodated the volume change of the conversion reaction type electrode.