In this work, magnetite nanoparticles (Fe3O4) that are well dispersed by a submicron sized carbon framework in a pomegranate shape are engineered using a flexible one-step spray pyrolysis strategy. Under inert gas atmosphere, the homogeneously mixed Fe3+ ions and chitosan (CS) molecules are in situ transformed to Fe3O4 nanoparticles and spherical nitrogen-doped carbon coating domains, respectively. Moreover, the obtained Fe3O4@C composite exhibits a unique submicron sized pomegranate configuration, in which favorable electric/ionic pathways have been constructed and the Fe3O4 nanoparticles have been effectively dispersed. When used as an anode electrochemical active material, the Fe3O4@C composite exhibits impressive lithium-ion storage capabilities, and maintains a reversible capacity of 500.2 mAh·g−1 after 500 cycles at a high current density of 1000 mA·g−1 as well as good rate capability. The strategy in this work is straightforward and effective, and the synthesized Fe3O4@C material has good potential in wider applications.