Monodisperse Fe3O4 polyhedrons enclosed by {100}/{111} facets with different area ratios were synthesized through the thermolysis of Fe(acac)3 by effectively tuning reaction temperature and time to mediate the adsorption of oleic acid (OA) on the crystallite surfaces, and utilized as high rate (≥1 A g−1) anode materials for lithium ion batteries (LIBs). The electrochemical results show that Fe3O4 octahedrons with highly reactive {111} facets possess the best high rate cycling performance compared to that of cuboctahedrons and cubes, characterized by a high 300th discharge capacity of 785.1 mAh g−1 at 1 A g−1 and the best rate capability of 657.7 mAh g−1 when cycled at 4 A g−1. These results prove that the surface structure of Fe3O4 polyhedrons significantly influence the property of Fe3O4 nanocrystal materials and hence their electrochemical performance though the morphology may be destroyed during cycling. These insights are helpful for the further understanding of Fe3O4 anode materials and provide a simple and practical route to design high rate anode materials for lithium-ion batteries.