It is necessary to understand the site seismic response for seismic design and post-earthquake damage assessment of structures in seismically active regions. In cold regions, the presence of layered frozen soil not only affects the ground motion characteristics but also influences the seismic response of structures on these sites. This study aims to investigate the effect of frozen soil site conditions on ground motion characteristics in cold regions through shaking table tests using a laminar shear box equipped with a soil freezing system. The seismic acceleration response, displacement response, and dynamic shear stress-strain relation were analyzed for both unfrozen and frozen soil sites under various seismic waves with different intensities. The existence of the frozen soil layer has been observed to mitigate ground motion during earthquakes, resulting in a reduced peak ground acceleration compared with the unfrozen soil site. If an earthquake occurs, the high-frequency waves will be attenuated by the frozen soil layer, which possesses a dominant frequency lower than that of the unfrozen soil site. Moreover, the energy dissipation capacity of the frozen soil site is larger than that of the unfrozen soil site during earthquakes. By combining the Fourier spectral ratio curves, it can be inferred that different input ground motions have varying effects on the seismic response of both unfrozen and frozen sites. These findings serve as valuable references for seismic design of structures in cold regions.