Femtosecond laser-induced periodic surface structures (LIPSS) have several applications in surface structuring and functionalization. Three major challenges exist in the fabrication of regular and uniform LIPSS: enhancing the periodic energy deposition, reducing the residual heat, and avoiding the deposited debris. Herein, we fabricate an extremely regular low-spatial-frequency LIPSS (LSFL) on a silicon surface by a temporally shaped femtosecond laser. Based on a 4f configuration zero-dispersion pulse shaping system, a Fourier transform limit (FTL) pulse is shaped into a pulse train with varying intervals in the range of 0.25–16.2 ps using periodic π-phase step modulation. Under the irradiation of the shaped pulse with an interval of 16.2 ps, extremely regular LSFLs are efficiently fabricated on silicon. The scan velocity for fabricating regular LSFL is 2.3 times faster, while the LSFL depth is 2 times deeper, and the diffraction efficiency is 3 times higher than those of LSFL using the FTL pulse. The formation mechanisms of regular LSFL have been studied experimentally and theoretically. The results show that the temporally shaped pulse enhances the excitation of surface plasmon polaritons and the periodic energy deposition while reducing the residual thermal effects and avoiding the deposition of the ejected debris, eventually resulting in regular and deeper LSFL on the silicon surface.