Local structures of ion-beam-synthesized amorphous Fe-Si thin layers and their microstructural changes upon thermal annealing have been examined using transmission electron microscopy (TEM) . Atomic pair-distribution functions extracted from electron diffraction patterns revealed that the nature of short-range order in amorphous Fe-Si thin layer can be well described by the atomic arrangements of crystalline iron silicides. The amorphous Fe-Si crystallized into β-FeSi2 after annealing at 1073 K for 2 h, and most of defects were successfully removed. We discussed the recrystallization process of amorphous Fe-Si thin layers as well as the growth mechanism of β-FeSi2 thin layer formed in high-dose Fe ion implanted Si.