Porous Fe3O4/carbon microspheres (PFCMs) were successfully fabricated via a facile electrospray method and subsequent heat treatment, using ferrous acetylacetonate, carbon nanotubes (CNTs), Ketjen black (KB), polyvinylpyrrolidone (PVP), and polystyrene (PS) as raw materials. The porous carbon sphere framework decorated with well-dispersed CNTs and KB exhibits excellent electronic conductivity and acts as a good host to confine the Fe3O4 nanoparticles. The abundant mesopores in the carbon matrix derived from polymer pyrolysis can effectively accommodate the volume changes of Fe3O4 during the charge/discharge process, facilitate electrolyte penetration, and promote fast ion diffusion. Moreover, a thin amorphous carbon layer on the Fe3O4 nanoparticle formed during polymer carbonization can further alleviate the mechanical stress associated with volume changes, and preventing aggregation and exfoliation of Fe3O4 nanoparticles during cycling. Therefore, as anode materials for lithium-ion batteries, the PFCMs exhibited excellent cycling stability with high specific capacities, and outstanding rate performances. After 130 cycles at a small current density of 0.1 A·g–1, the reversible capacity of the PFCM electrode is maintained at almost 1, 317 mAh·g–1. High capacities of 746 and 525 mAh·g–1 were still achieved after 300 cycles at the larger currents of 1 and 5 A·g–1, respectively. The optimized structure design and facile fabrication process provide a promising way for the utilization of energy storage materials, which have high capacities but whose performance is hindered by large volume changes and poor electrical conductivity in lithium or sodium ion batteries.