Femtosecond (fs) laser processing has received great attention for preparing novel micro-nano structures and functional materials. However, the induction mechanism of the micro-nano structures induced by fs lasers still needs to be explored. In this work, the laser-induced periodic surface structure (LIPSS) of monocrystalline silicon (Si) under fs laser irradiation is investigated. Three different layers named amorphous silicon (a-Si) layer, transition layer, and unaffected Si layer are observed after laser irradiation. The a-Si layer on the surface is generated by the resolidification of melting materials. The unaffected Si layer is not affected by laser irradiation and maintains the initial atomic structure. The transition layer consisting of a-Si and unaffected Si layers was observed under the irradiated subsurface. The phase transition mechanism of Si irradiated by fs laser is “amorphous transition”, with the absence of other crystal structures. A numerical model is established to describe the fs laser-Si interaction to characterize the electronic (lattice) dynamics of the LIPSS formation. The obtained results contribute to the understanding of fs laser processing of Si at the atomic scale as well as broaden the application prospects of fs laser for treating other semiconductor materials.