In this work, carbon-coated MnFe2O4 nanoparticle (NP) hollow microspheres are fabricated by a facile emulsion-based assembly method followed by in situ ligand carbonization. Specifically, MnFe2O4 NPs stabilized by oleic acid (OA) are the primary building blocks to assemble hollow microspheres, while the subsequent carbonization of OA ligands leads to the formation of uniform carbon coatings without degrading the ordering of NPs. As anode materials for lithium-ion batteries, such MnFe2O4 NP hollow composite microspheres exhibit significantly improved electrochemical performance in comparison with their solid counterparts and most MnFe2O4-based anodes reported to date, retaining a high reversible capacity of 730mAhg−1 after 300 cycles at a current density of 2Ag−1. Furthermore, even when tested at an ultrahigh rate of 10Ag−1, MnFe2O4 NP hollow microspheres can still deliver a high specific capacity of 433mAhg−1. The superior performance of MnFe2O4 NP hollow microspheres is attributable to their hollow superstructure, close-packed configuration of the constituent NPs, and uniform carbon coatings, which facilitate lithium-ion and electron transport while simultaneously alleviating the drastic volumetric change during cycling. Our work establishes that the optimized MnFe2O4 anode material offers great promise for high-performance lithium-ion batteries.