The trigger for seismic damage may be determined by researching the characteristics of strong ground motion in loess hill valleys under earthquake action. In this paper, considering the geomorphic characteristics of the Loess Plateau, typical models of dynamic numerical analysis are established. In a valley site influenced by rugged terrain and a loess covering layer, the seismic response was analyzed by inputting seismic waves with different amplitudes, frequency spectrum characteristics, and duration. The results show that the coupling action of the soil layer and terrain controls the PGA change on the ground surface and that the change trend is complex. Under the input of the same wave with a different amplitude and compared with monitoring points in the bedrock valley, the spectrum amplitude of the ground motion at the loess-covered valley points increased, and the peak moved to a high frequency. Under the input of different seismic waves, the natural frequencies of different parts of the site were influenced by the terrain and the soil layers; the size and amplitude of the ground motion frequency spectrum was not only related to the natural frequency spectrum of the site and topographic change, but also to the spectral components of the input seismic wave. At the same site, with the same PGA and seismic spectrum characteristics of the input wave, the output seismic spectrum shape showed similar characteristics. As the seismic duration increased, the earthquake energy was concentrated in the field near the natural frequency, which may lead to an increase in the vibration amplitude of buildings with a corresponding frequency.