The seismic input is the basis for the seismic safety analysis of dams, but current seismic input methods have not reasonably considered the influence of canyon scattering effects on the dynamic response of dams. In this paper, the total motion field of the canyon is deconstructed into the free field of a uniform half space and the scattering field of the canyon and they are obtained separately. The indirect boundary integral equation method (IBIEM) is used to determine the scattering field of the canyon, which is superimposed with the free field to obtain the seismic ground motion field (total motion field) of the canyon. The accuracy of the total motion field of the canyon is verified through reference solutions. In the finite element analysis of seismic ground motion field in the canyon, the total motion field at the truncation boundary of the canyon foundation is transformed into the equivalent seismic input loads and the interior of the canyon are simulated using the finite element method (FEM). Then, based on the wave input for the free field combined with the viscoelastic artificial boundary, a new wave input method for the total motion field combined with the viscoelastic artificial boundary is established. The seismic wave input method based on the finite element-indirect boundary integral equation method is applied to numerically determine the seismic response of a trapezoidal canyon. The differences in the seismic response of the canyon under free-field input and total motion field input are discussed. The results show that there is a certain deviation between the displacement and waveform obtained from the free-field input and the solutions obtained from the indirect boundary integral equation method. There is a large error for a large angle of incidence, and the errors increase with increasing seismic wave frequency. When the incident angle is 60°, the maximum error in the frequency domain reaches 92.3 %, and the maximum error in the time domain reaches 250 %. The displacement amplitude and waveform of the canyon obtained from the total motion field input showed agreement with the results of the indirect boundary integral equation method. The wave input method established in this paper has high calculation accuracy and reasonably considers the scattering effect of canyons, which provides a basis for more accurate predictions of the seismic response of dams on canyon foundations.