As anode materials for lithium ion batteries, metal oxides have large storage capacity. However, their cycle life and rate capability are still not suitable for commercial applications. Herein, 3D hierarchical Fe₃O₄ spheres associated with a 5–10 nm carbon shell were designed and fabricated. In the constructed architecture, the thin carbon shells can avoid the direct exposure of encapsulated Fe₃O₄ to the electrolyte and preserve the structural and electrochemical integrity of spheres as well as inhibit the aggregation of pulverized Fe₃O₄ during electrochemical cycling. The hierarchical structure formed by the bottom-up self-assembly approach can efficiently accommodate the mechanical stress induced by the severe volume variation of Fe₃O₄ during lithiation–delithiation processes. Moreover, the carbon shell together with the structure integrity and durability endows the favorable high conductivity and efficient ion transport. All these features are critical for high-performance anodes, therefore enabling an outstanding lithium storage performance with a long cycle lifespan. For instance, such an electrode could deliver a capacity of 910 mA h g⁻¹ even after 600 cycles with a discharge–charge rate of 1 A g⁻¹. In addition, this effective strategy may be readily extended to construct many other classes of hybrid electrode materials for high-performance lithium-ion batteries.