Three dimensional (3D) porous self-assembled MoO2/graphene microspheres are successfully synthesized via microwave-assisted hydrothermal process in a short reaction time followed by thermal annealing. Such rationally designed multifunctional hybrid nanostructure is constructed from interconnected MoO2 nanoparticles (3–5 nm), which is self-assembled into ordered nanoporous microspheres via strong electrostatic attraction between graphene sheets and MoO2 nanoparticles. The MoO2/graphene hybrid structure delivers a high reversible capacity with significantly enhanced cycling stability (∼1300 mAh g−1 after 80 cycles at C/10 rate) and excellent rate capability (913 and 390 mAh g−1 at 2C and 5C rates, respectively), when used as an anode material. The microspheres are interconnected and well encapsulated by the flexible graphene sheets, which not only accommodates large volume change but also increases the electrical conductivity of the hybrid structure. Moreover, nanoporous voids present in the 3D framework facilitate effective electrolyte penetration and make a direct contact with the active MoO2 nanoparticles, thereby greatly enhancing lithium ion transport. The strategic combination of self-assembly, nanoporous voids, 3D network and intriguing properties of graphene sheets provides excellent electrochemical performance as anode materials for Lithium ion battery applications.