The effective permittivity of composites containing Fe-Cu-Nb-Si-B nanocrystalline micro flakes has been studied within 0.5–10 GHz. Obvious differences in microwave permittivity have been observed for composites consisting of large flakes (size range: 23–111 μm, average thickness: 4.5 μm) and small flakes (size range: 3–21 μm, average thickness: 1.3 μm). Both the real part and imaginary part of permittivity of large flake composite are much larger than these small one in a given frequency. And faster decrease of permittivity with the increasing frequency can be observed for large flake composite than that of small one. These differences in permittivity spectra of different flakes have been explained from the perspective of interfacial polarization and ac conductivity. The assumption that more extensive ohmic contact interface between large flakes and matrix has been validated by the fittings and the calculated percolation threshold. Meanwhile, the permeability spectra of both composites also have been studied by Lorentzian dispersion law. The broadened spectra can be attributed to the distribution of magnetic anisotropy fields of two kinds of ferromagnetic phases in the particles. Finally, the composite containing the small flakes exhibits better electromagnetic wave absorption properties.