CoFe alloy nanoflakes (NFs) with diameter and thickness on nanoscale were prepared by hydrogen-thermal reduction in CoFe2O4 flakes at 400 °C for 60 min. The effective complex permittivity and permeability of CoFe alloy NFs/paraffin composites were measured and compared with that of CoFe alloy nanoparticles (NPs)/paraffin composites. Due to the two-dimensional shape character, the real part of permittivity and permeability of CoFe alloy NFs was rather higher than that of CoFe alloy NPs. Electromagnetic wave absorbing (EMA) performance of both CoFe alloy NFs and NPs was evaluated by using transmission line theory. The effective EMA band position of the coating with CoFe alloy NFs as fillers was found to locate in the range of 2–4 GHz, while the effective EMA band position of the coating containing CoFe alloy NPs as fillers was located in the range 8–18 GHz. A maximum reflection loss (RLmax) of −57.8 dB was achieved in a coating containing CoFe alloy NFs as fillers, which is much higher than the −16.6 dB of coatings with CoFe alloy NPs.