Time-frequency joint analysis was used to investigate the seismic response of rock slopes containing weak structural planes. Four three-dimensional finite element models containing infinite element boundaries were modelled: homogeneous slope, anti-dip slope, bedding slope, and block slope models. The material of the models was elastic material. The influence of the structural planes on the seismic responses of the slopes was systematically analyzed. The results of time-frequency joint analysis show that the structural planes impact the propagation characteristics of the waves and the dynamic amplification effect of the slopes. The wave propagation characteristics and peak ground acceleration distribution of the block slope model are more complex than those of the other models. The influence of structural planes on the amplification effect of the slopes is discussed. Additionally, according to frequency-domain analysis, structural planes have a small impact on the natural frequencies and the peak Fourier spectrum amplitude distribution of the slope but have a significant influence on its dynamic deformation characteristics. The natural frequencies of slopes can be obtained by using modal analysis and Fourier spectrum analysis. The relationships between the natural frequencies of the slopes and their dynamic deformation characteristics were analyzed; in particular, the impacts of low-order and high-order natural frequency on the deformation of the surficial slope were investigated. The applicability of the energy spectrum in the evaluation of the dynamic deformation characteristics of slopes was discussed. The effects of structural planes on the seismic failure mode of the slopes are identified according to the analyses of the dynamic responses of the slopes.