Graphene-encapsulated hierarchical metal oxides architectures can efficiently combine the merits of graphene and hierarchical metal oxides, which are deemed as the potential anode material candidates for the next-generation lithium-ion batteries due to the synergistic effect between them. Herein, a cationic surfactant induced self-assembly method is developed to construct 3D Fe3O4@reduction graphene oxide (H-Fe3O4@RGO) hybrid architecture in which hierarchical Fe3O4 nano-flowers (H-Fe3O4) are intimately encapsulated by 3D graphene network. Each H-Fe3O4 particle is constituted of rod-shaped skeletons surrounded by petal-like nano-flakes that are made up of enormous nanoparticles. When tested as the anode material in lithium-ion batteries, a high reversible capacity of 2270 mA h g−1 after 460 cycles is achieved under a current density of 0.5 A g−1. More impressively, even tested at a large current density of 10 A g−1, a decent reversible capacity of 490 mA h g−1 can be retained, which is still higher than the theoretical capacity of traditional graphite anode, demonstrating the remarkable lithium storage properties. The reasons for the excellent electrochemical performance of H-Fe3O4@RGO electrode have been discussed in detail.