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To solve seismic wave scattering by a large-scale three-dimensional (3-D) hill topography, a fast parallel indirect boundary element method (IBEM) is developed by proposing a new construction method for the wave field, modifying the generalized minimum residual (GMRES) algorithm and constructing an OpenMP plus MPI parallel model. The validations of accuracy and efficiency show that this method can solve 3-D seismic response of a large-scale hill topography for broadband waves, and overcome the weakness of large storage and low efficiency of the traditional IBEM. Based on this new algorithm architecture, taking the broadband scattering of plane SV waves by a large-scale Gaussian-shaped hill of thousands-meters height as an example, the influence of several important parameters is investigated, including the incident frequency, the incident angle and the height-width and length-width ratio of the hill. The numerical results illustrate that the amplification effect on the ground motion by a near-hemispherical hill is more significant than the narrow hill. For low-frequency waves, the scattering effect of the higher hill is more pronounced, and there is only a single peak near the top of the hill. However, for high-frequency waves, rapid spatial variation of displacement amplitude appears on the hill surface.