At present, some high arch dam projects in the domestic and overseas have already experienced the phenomenon of valley deformation after impoundment, which not only affects the change of arch dam properties, but also has been proven to affect the normal operation of the downstream energy dissipation buildings. In order to analyze the effect of valley deformation on the operation of energy dissipation buildings in Baihetan Hydropower Station, we adopted the boundary displacement method for the finite element analysis, simulated the stress state of the plunge pool with an inverted-arch slab under maintenance condition (no water) and normal operation condition with different valley deformation amplitudes, and analyzed the effect of different arrangements of elastic joints on the stress state of the plunge pool under the effect of valley deformation. The results show that with the increase of valley deformation, the stress of the pool also increases; when the valley deformation of the top of the pool is less than or equal to 50 mm, the safety of the plunge pool with a seamless structure is in control, and the impoundment can further reduce the influence of valley deformation on the adverse stress of the pool structure, whereas the setting of elastic joints may increase its adverse stress.