Femtosecond-laser modified silicon materials have excellent optoelectronic properties and device application prospects, thus capturing pervasive interest from academia and industry. Nevertheless, efficiently achieving large-area uniform modification on silicon surfaces with Gaussian laser beams, especially fabricating evenly and extensively distributed microcone structures, remains a formidable obstacle. Our theoretical and experimental investigations demonstrate that the pulse-shaping technique effectively regulates the light–matter interaction, leading to improved surface uniformity through nonlinear and linear modulation. A large-area uniformly distributed microcones are prepared on the silicon surface through pure temporal modulation of the pulse. In addition, the method is easy to implement and has good compatibility. These findings carry significant implications for advancing the femtosecond-laser processing technology and promoting the industrial utilization of modified silicon materials, including photoelectric detection and solar cell fields.