Due to the complexity of excavation and groundwater seepage, the behavior of foundation pits is not yet well understood. In this paper, based on three-dimensional (3D) Biot’s consolidation theory and nonlinear Duncan-Chang’s model, finite element equations considering the coupling of groundwater seepage and soil skeleton deformation during excavation are deduced and a corresponding three-dimensional finite element program is developed. Using the program, the influence of soil permeability, rigidity and tiers of supports, rigidity of retaining wall and construction period of excavation on ground surface settlement, wall horizontal displacement and pit base heave are analyzed in detail. Some useful conclusions are drawn by analyzing the influence of these factors on the excavation deformations, which are very significant for guiding design and construction of excavations.