The present invention provides a terahertz modulator based on a silicon-based microstructure on SOI and its preparation method and modulation system. The terahertz modulator includes from bottom to top: the underlying Al 2 o 3 Substrate, SiO 2 Isolation layer, silicon-based microstructure, Al 2 o 3 passivation layer, silicon-based microstructure in SiO 2 Periodically arranged on the isolation layer, each silicon-based microstructure includes two layers of square Si-based step structures, and the modulation system includes: a semiconductor laser, a laser modulator, a terahertz modulator, a terahertz radiation source, and a terahertz detector. The present invention For terahertz waves from 0.4THz to 0.85THz, the reflectivity is below 22%, reaching the lowest 18% at 0.82THz, which can significantly reduce the reflectivity of modulation devices to terahertz waves and improve the utilization of terahertz waves; in power Under the irradiation of 1200mw 808nm laser, the modulation depth reaches 64.5%. Compared with the traditional silicon-based terahertz modulator, the terahertz imaging diffusion area effectively improves the resolution in the imaging system to more than 21.9%.