We report the creation of a functional nanostructure on a Si crystal surface by 200 keV C60(++) cluster ion bombardment (CIB). We found that the modified layer produced by CIB includes two sublayers with different nanostructures. The top 24-nm-thick sublayer is an agglomeration of 5-nm-sized amorphous Si nanodots (a-Si NDs). The deeper 10-nm-thick sublayer is a transient layer of disordered Si as an interface between the a-Si top sublayer and the bulk Si(100). The top a-Si sublayer and the nc-Si transient layer are formed by the local heating effect and shock wave effect, respectively, induced by the cluster ion impacts. The photoluminescence (PL) spectra of the CIB-modified Si samples revealed an emission line centered at a photon energy of 1.92 eV. The absorption spectra of the modified samples exhibit enhanced light absorption at this photon energy. The parameters of the PL line require ascribing the emission origin to the quantum-confinement-induced optical transitions in the a-Si nanodots. The core-shell structure of a-Si NDs is confirmed by detection of an additional PL line centered at 2.5 eV. Analysis of the Rutherford backscattering (RBS) and the PL spectra implies the existence of -Si--O- bonds in the nanodot outer shells, which are responsible for the additional PL line. The obtained results demonstrate the valuable potential of CIB for the controllable fabrication of Si surface nanostructures, which is attractive for optoelectronics and nanoelectronics. The obtained results elucidate the evolution of structure modification occurring in silicon due to the injection of energetic C60 cluster ions with an energy of hundreds of keV.