The practical application of metal oxides (e.g., Fe3O4) as anode materials for lithium-ion batteries is hindered by their poor electrical conductivity and severe volume change in spite of their high theoretical capacities and abundance nature. In this work, uniform yolk-shell Fe3O4@nitrogen-doped carbon composites are synthesized by combining polymerization of o-phenylenediamine (oPD) with core-shell Fe3O4@SiO2 nanospheres, followed by pyrolysis of poly (o-phenylenediamine) (PoPD) and removal of silica. This novel composites exhibit superior lithium storage capacity and cycling stability due to their unique yolk-shell structure and nitrogen-doped carbon shell, which provide ample space to accommodate the volume expansion of Fe3O4 nanoparticles, prevent the aggregation of Fe3O4 nanoparticles, and enhance the electron conductivity during cycling. This newly developed method can be employed in other yolk-shell structural design of hybrids with high-performance for lithium-ion or lithium-sulfur batteries.