Seismic wave propagation in irregular terrain sites can lead to changes in the amplitude and spectral components of ground shaking on the site surface, resulting in spatial and temporal differences in ground shaking at different locations on the site surface. The oblique incidence of seismic waves will exacerbate this difference, resulting in a more complex seismic response for bridge structures on the site. By constructing the site and bridge models, and taking the bridge structural support as the observation point, we calculate and analyze the variation rule of ground vibration on the surface of the site with different incidence angles in the river valley terrain. Further take the ground vibration at the bridge piers on the site surface as the input, simulate the structural response of the bridge structure with multi-point non-uniform ground vibration input, and explore the influence of mountain valley topography on the seismic response of high pier and large-span bridges. The computational analysis shows that: (1) the incidence angle of seismic wave significantly changes the degree of influence of topographic effect on the seismic response of bridge structure; (2) the non-uniformity of ground shaking caused by topographic effect leads to the complexity of the internal force response of the bridge structure, and the maximum increase of the internal force of the bridge structure is 388% compared with the uniform excitation. It is suggested that the seismic design of bridge structures with high piers and large spans across river valleys should fully consider the influence of topographic effect on the structural response of bridges, and should pay enough attention to the influence of seismic wave incident direction and its uncertainty.