Based on multipoint ground motion input method and an equivalent visco-elastic constitutive model for rockfill, a semi-analytical method is used to conduct dynamic analysis of high concrete face rockfill dams (CFRD) subject to non-uniform input motion. The validation of the calculation method is first conducted in the frequency domain. Under the condition that the acceleration time histories on the surface of the free field are assumed to be consistent for different modes of non-uniform and uniform seismic input, the following main conclusions can be drawn. The seismic response to the non-uniform input is generally smaller than that to the uniform input. The dynamic tensile stresses become obviously larger at the waterstops (the seepage control system of CFRD) for the non-uniform input than for the uniform one. The seismic responses of the high CFRD to the non-uniform input are characterized by the smaller in central part and the larger around the boundary. The seismic response of high CFRDs under the incidence of P, SV and SH waves are featured by the following several main facts and findings: With increasing incident angle for SH waves, the response intensity shows almost constant. There exists a critical angle for SV waves. When the incident angle is close to the critical angle, the response intensity first increases and then decreases sharply, and before that, the intensity is nearly constant, while after that, the intensity keeps decreasing. There exists a feature angle for P waves. When the incident angle is smaller than it, the response intensity is almost constant, while when larger, the intensity keeps decreasing.