Several hundred strong motion records from two bedrock stations and two class Ⅲ stations from the KiK-Net in Japan were used to analyze ground motion features, the relationship between Fourier spectrum dominant frequency and magnitude or distance, and the effect of shallow surface rock and soil layers on ground motion. At the bedrock stations, both underground and at the surface, the Fourier spectrum dominant frequencies for three components decreased with increasing magnitude or distance, and exhibited similar values and distribution. However, at class Ⅲ sites, only the underground sites displayed a decrease in their three-component Fourier spectrum dominant frequencies over increasing magnitudes or distances. At these class Ⅲ sites, the Fourier spectrum dominant frequencies displayed significantly different values and distributions between the underground and surface ground motions, and the changes are different between the ground motions at stations with different soil conditions. These results indicate that hard bedrock has little effect on ground motion; however, an overlying soil layer on the bedrock has a profound and uncertain effect on ground motion characteristics.