The damaged layer formed on a Si(100) surface by low-energy (300-600 eV) rare-gas (Ne, Ar, or Xe) ion bombardment was analyzed in situ by x-ray photoelectron spectroscopy (XPS). The XPS analysis showed that an amorphous Si (a-Si) layer with a thickness of 1-3 nm was formed and saturated by a dose of 10¹⁵cm^-2 irrespective of the ionic species. It also showed that the thickness increased linearly with the ion energy and that Ne ions formed the thickest a-Si layer. The XPS analysis has been confirmed by transmission electron microscopy. The process of the a-Si layer formation with a small dose of ions can be explained in terms of the Poisson process. As a result, the size of an a-Si region formed by single ion bombardment was estimated. The region, which is supposed to have a cylindrical shape, has a radius of 0.2-0.4 nm and a height of 1-3 nm for each ionic species and energy. In situ XPS analysis of the Si surface bombarded with ion beams revealed the growth process of the a-Si layer in addition to the dependence of the thickness on the ionic species, energy, and dose.