CoFe2O4 flower-like microspheres are prepared via a surfactant- and template-free method, involving the controlled hytrothermal synthesis firstly and a subsequent thermal decomposition treatment. The microspheres with diameters of 3–4 μm are characterized by the assembly of numerous porous and inter-connected lamella structures. Lithium-ion batteries electrodes based on the as-prepared CoFe2O4 microspheres show a high specific capacity of 733.5 mAh g−1 after 50 cycles at a current density of 200 mA g−1 and a good cyclic stability, as well as excellent rate capability. The enhanced electrochemical performance can be attributed to the hierarchical microsphere structure with high sufficient interfacial contact area between the microspheres and electrolyte, the short diffusion distance of Li+, better accommodation of structural stress and volume change with the lithiation/delithiation process. It is suggested that the CoFe2O4 microsphere is one of the most promising candidates for high-performance lithium-ion batteries.