Metal silicides are complicated materials due to the complex phase behavior between metals and silicon and the complex stoichiometries and structures of their resulting compounds. Iron silicide nanoparticles with various phases have been successfully controlled and synthesized via thermal annealing of a core–shell structure Fe–FeSi2 sample at atmospheric pressure under Ar and H2 atmospheres. The results from X-ray diffraction, transmission electron microscopy, and Mössbauer spectroscopy indicated that the crystal transformation proceeded from Fe–FeSi2 to FeSi and Fe3Si with increasing the annealing time and temperature. The samples presented ferromagnetic properties, and the saturation magnetization changed with the annealing temperature due to the aggregation of the nanoparticles. This thermal annealing method can also be applied to the synthesis of other metal silicides with different metal/silicon ratios that are otherwise difficult to synthesize.