Establishing an ultra-high-precision link for time–frequency comparisons between satellites and ground stations is critically important. This endeavor is fundamental to the advancement of pioneering space science exploration and the development of a robust space-based time–frequency system featuring ultra-high-precision space atomic clocks. In response to the requirements for assessing the long-term stability of high-precision space atomic clocks, we have designed and implemented a satellite–ground microwave time–frequency comparison system and method based on a three-frequency mode. Ground-based experimental results demonstrate that the equipment layer can achieve a satellite–ground time comparison accuracy better than 0.4 ps (RMS), with the equipment delay stability (ADEV) for all three frequencies being better than 8 × 10−18 at 86,400. By leveraging the ground-based experimental results, we constructed a satellite–ground time–frequency comparison simulation and verification platform. This platform realizes ultra-high-precision satellite–ground time–frequency comparison based on the China Space Station (CSS). After correcting various transmission delay errors, the satellite–ground time comparison achieved an accuracy better than 0.8 ps and an ADEV better than 2 × 10−17 at 86,400. This validation of our novel satellite–ground time–frequency comparison system and method, capable of achieving an 10−17 magnitude stability, is not only a significant contribution to the field of space time–frequency systems but also paves the way for future advancements and applications in space science exploration.