Fe3O4 is considered as potential anode material for lithium-ion batteries with excellent lithium storage performance, but there are still issues of poor conductivity and volume expansion during charging and discharging. In this paper, L-arginine, p-phenylenediamine, and iron(III) nitrate nonahydrate were used as raw materials to synthesize iron-doped L-arginine polymer (W-Fe3O4@NC precursor) through solvent thermal reaction. Subsequently, the waxberry-like carbon-coated Fe3O4 composite (W-Fe3O4@NC) was prepared by carbonization of the W-Fe3O4@NC precursor. The morphology, surface chemical structure, porosity, and electrochemical performance as lithium-ion battery anode of W-Fe3O4@NC were characterized. Benefit from the unique waxberry-like shape, beneficial nitrogen doped, highly dispersed Fe3O4 nanoparticles, and uniform carbon coating, the specific capacity of W-Fe3O4@NC reaches to 815.1 mAh/g after 800 cycles at a current density of 1 A/g and still remains 232 mAh/g at a current density of 5 A/g, which surpass those of NC and commercial Fe3O4 nanoparticles, demonstrating excellent cycling stability and rate performance.