Efficient energy storage systems based on rechargeable lithium-ion batteries (LIBs) represent the most leading technology in the field of portable devices market. Nanostructured electrode materials possess compelling opportunities for high-performance LIBs, but it's still the main challenge to ensure the structural integrity of the electrodes over harsh discharge-recharge cycles. Here, we present a general approach, combining self-assembly process, in-situ substitution, and thermal annealing, for the fabrication of a 3D heteroarchitecture built from nanosized spinel ferrites (MFO, denoted as MFe2O4, M = Mn, Ni, Cu, Co) and graphitic carbon nitride covalently functionalized nitrogen-doped graphene (CN-NG). This typical 3D architecture could possess a series of distinctive structural advantages, including: (i) sufficient hierarchical pores and channels for the rapid access of electrolytes, (ii) plentiful topological defects introduced by lamellar g-C3N4 nanoflakelets for the ultrafast absorption and diffusion of lithium ions, (iii) incorporation of structural nitrogen in graphene to modulate the electronic structure for boosting the electron transport and providing extra mechanism for lithium storage, (iv) uniformly distributed MFO nanoparticles with large amounts of active centers and high reversible capacities, (v) strong covalent C-N bonding and metal-support interaction for guaranteeing the long-term electrochemical cyclability, all of which are conducive to accelerating the improvement of lithium storage properties. As a consequence, significantly high reversible capacities of 1032, 919, 1008, and 1105 mAh g−1 are obtained for 3D MnFe2O4/CN-NG(0.4), 3D NiFe2O4/CN-NG(0.4), 3D CoFe2O4/CN-NG(0.4), and 3D CuFe2O4/CN-NG(0.4), respectively, at a current density of 0.1 A g−1. Especially, 3D MnFe2O4/CN-NG(0.4) presents a capacity retention of 73% at a high current density of 1 A g−1 even after 800 cycles, as well as excellent rate capability and reliable long-term cycling stability. It is anticipated that the synthetic strategy present here can be further extended to the construction of various 3D heteroatom-doped carbonaceous nanomaterials that contain metals or metal oxides, which offers new possibilities in the fabrication of advanced supports for maximum utilization, alleviating volume variation and the particle fracture of active materials in LIBs.