Engineering bead-on-string architectures with refined interfacial interactions and low ion diffusion barriers is a highly promising but challenging approach for lithium/sodium storage. Herein, a spindle-chain-structured Fe-based metal organic frameworks (MIL-88A) self-sacrificial template was constructed via the seed-mediated growth of Fe3+ and fumaric acid in an aqueous solution, which is an environmentally friendly synthesis route. The seed-mediated growth method effectively segregates the nucleation stage from the subsequent growth phase, offering precise control over the growth patterns of MIL-88A through manipulation of kinetic and thermodynamic parameters. The structural diversity, fast ion/electron diffusion, and unique interfaces of whole anodes are simultaneously enhanced through optimization of the spindle-chain structure of Fe2O3@N-doped carbon nanofibers (FO@NCNFs) at the atomic, nano, and macroscopic levels. Benefiting from their heteroatom-doping conductive networks, porous structure, and synergistic effects, FO@NCNFs exhibit a remarkable rate performance of 167 mAh g-1 at 10 A g-1 after 2000 cycles for lithium-ion batteries (LIBs) and long-term cycling stability with a sustained capacity of 260 mAh g-1 at 2 A g-1 after 2000 cycles for sodium-ion batteries (SIBs). This versatile approach for fabricating bead-on-string architectures at both the nanoscale and macroscale is promising for the development of high-energy–density and high-power-density electrode materials.