The deformation of dams and reservoir basin of upper reservoir at the pumped storage power station can affect the anti-seepage structure and effects. The dam of upper reservoir at a pumped storage power station is a concrete faced rockfill dam and the impermeable material of reservoir bottom is composite geo-membrane. Aiming at the dam and the reservoir basin, the 3-D non-linear finite element model was developed to simulate the filling process of the dam and backfill and the storage process of the reservoir. The deformation and stress of the dam, backfill, and composite geo-membrane were analyzed, and the rationality of the structural design was demonstrated. The results showed that the displacement distribution and stress distribution of the dam were reasonable. The option on composite geo-membrane was reasonable as the safety factors met standard requirements. The composite geo-membrane can adapt to the deformation of the backfill very well without the occurrence of disengaging phenomenon. Emphasis should be put in the dividing area of backfill and bedrock as the gradient of the normal displacement equipotential line of composite geo-membrane was large and tensile stress was high.