In saturated fine-grained soil, the development and dissipation of excess pore water pressure (EPWP) during and after pile jacking change the effective stress of the surrounding soil, and thereby affect the pile set-up. In this paper, the entire process of steel-pipe pile jacking (the installation process and the subsequent consolidation phase) is simulated with three-dimensional (3D) finite element models, considering the pore water effect. After the model verification, a comprehensive numerical analysis was performed to investigate the development and dissipation of EPWP, changes in soil stress state, and the side shear resistance of pile with time after installation. On this basis, not only the influence of ks, cu, E, and OCR on EPWP generation during pile jacking and subsequent soil consolidation effect after pile installation but also the correlation between pile set-up and EPWP dissipation is investigated.