We present a facile and simple method for the large-scale synthesis of octahedral iron oxide nanocrystals (Fe3O4 ONCs) on the reduced graphene oxide nanosheets (rGO NSs). The Fe3O4-ONCs embedded on the rGO NSs surfaces (Fe3O4-ONCs@rGO hybrids) are synthesized by microwave assisted. The Fe3O4 nanoparticles (Fe3O4 NPs) decorated rGO NSs (Fe3O4-NPs@rGO hybrids) are also synthesized using same method for comparative studies in lithium ion storage. During the synthesis process, rGO NSs served as the structural platform to embed the positively charged Fe3O4-ONCs on the basis of the electrostatic assembly followed by the microwave reduction of rGO NSs. Compared to Fe3O4-NPs@rGO, Fe3O4-ONCs@rGO hybrids shows superior electrochemical performance, including better cycling stability and rate performances, which may be attributed to the embedded structure of the nano-size Fe3O4-ONCs in rGO NSs. The electrochemical performances of the hybrids material as anode for lithium storage are evaluated by cyclic voltammetry and constant current charging and discharging. The synthesized Fe3O4-ONCs@rGO hybrids exhibited high lithium storage capacity, outstanding cycling stability (540 mAh g−1 after 120 cycles at 100 mA g−1). This low-cost and fast synthesis strategy may be employed in other embedded structured hybrids design for high-performance lithium batteries.