The seismic performance of large-span water transfer structures has become increasingly prominent with the growing number of water transfer projects in recent years. In this paper, the effect of differential ground motion caused by topographic effects on the seismic response of Longchuanjiang large-span water transfer inverted siphon in Central Yunnan Water Diversion Project is examined by establishing a three-dimensional finite element model with the calculated results of SH wave horizontal incidence, oblique incidence and vertical incidence as ground motion inputs. The results are compared with those under uniform excitation. Results manifest that differential ground motion in consideration of topographic effect has a significant impact on the force and deformation of important structural elements, and different structural components behave differently. The transverse force and deformation of steel pipes, piers and other elements under horizontal incidence is the largest, followed by that under oblique incidence, uniform excitation, and vertical incidence in sequence, while the differential seismic effect causes a reduction in the transverse internal force of the arch ring. The location of structural stiffness change is more sensitive to differential seismic effect. In conclusion, it is necessary to consider the topographic effect and the influence of incidence angle of ground motion in the seismic design of large-span water transmission inverted siphon structures.