We report self-organized periodic nanostructures on amorphous silicon thin films by femtosecond laser-induced oxidation. The dependence of structural periodicity on the thickness of silicon films and the substrate materials is investigated. The results reveal that when silicon film is 200 nm, the period of self-organized nanostructures is close to the laser wavelength and is insensitive to the substrates. In contrast, when the silicon film is 50 nm, the period of nanostructures is much shorter than the laser wavelength, and is dependent on the substrates. Furthermore, we demonstrate that, for the thick silicon films, quasi-cylindrical waves dominate the formation of periodic nanostructures, while for the thin silicon films, the formation originates from slab waveguide modes. Finite-difference time-domain method-based numerical simulations support the experimental discoveries.Graphical abstractSupplementary InformationThe online version contains supplementary material available at 10.1007/s12200-023-00071-6.