Carbon-encapsulated Fe3O4 nanoparticles (Fe3O4@C) with varied microstructures were produced by controlling the relative concentrations of glucose and iron nitrate hydrate in a hydrothermal process, followed by heat treatment in Ar atmosphere. Three Fe3O4@C nanocomposites with different particle sizes (mean diameter 31.2, 45.1 and 55.3nm) and Fe3O4 core size (26.8, 15.4 and 10.3nm) were investigated for lithium storage performance. The Fe3O4@C nanoparticles with 15.4nm Fe3O4 core exhibit excellent initial specific capacity (1215mAhg−1) and significantly improved cycling performance (806mAhg−1 after 100 cycles) and rate capability (573mAhg−1 at current density of 1500mAg−1), in comparison to the other Fe3O4@C composites. This superior performance is attributed to microstructural effects spawned from the pomegranate-like carbon coating architecture of the composite, the appropriate carbon content, and the optimized particle size of Fe3O4@C nanoparticles, which combined suppress the agglomeration and pulverization of Fe3O4 nanoparticle upon cycling and enhance the electrical conductivity of the Fe3O4 anode.