The deformation of a pumping station significantly impacts its performance and was a focal point during the design and construction phases. This study integrates the construction of a large-scale drainage pumping station, a project in the flood control and management of Chaohu Lake. Constitutive model parameters of soil at different depths were obtained and a three-dimensional finite element model encompassing the pumping station structure, lower soil layer, and prefabricated concrete pipe pile was developed. The finite element simulation results showed that foundation soil undergoes certain settlement deformation after pile construction, with settlement deformation of the foundation soil being 40 mm, 35 mm, 30 mm, and 2 mm for pipe pile lengths of 35 m, 40 m, 45 m, and when the pile bottom reaches the gravel layer, respectively. The maximum settlement deformations of the pumping station after concrete casting and metal structure installation under various pile lengths were 160 mm, 140 mm, 120 mm, and 40 mm, respectively. The maximum settlement deformation at the pump house section when the pile enters the lower gravel layer was approximately 36 mm, and the maximum Mises stress at the stress concentration area of the pumping station structure was about 60 MPa. These findings provide technical references for similar engineering pipe pile treatment projects.