Recently the introduction of performance-based design into infrastructure including pile foundation is on process. For performance-based design, it is necessary to develop a practical prediction method for long-term displacements of pile foundation. In this paper, soil-water coupled analyses with FEM-FDM method are conducted to evaluate the long-term displacements of pile foundation installed in soft clayey ground. The analytical target is the actual pile foundation of road viaduct planned to be constructed in Niigata Prefecture, Japan. As constitutive model for ground, subloading t(ij) model is adopted, which is a simple elasto-plastic model for normally and over consolidated soils. Further more, centrifuge model tests are conducted to verify the validity of the numerical analyses. As the conclusion of a series of analyses and centrifuge model tests, following aspects are clarified; 1) the long-term behaviour of pile foundation; 2) the influence of the thickness of bearing layer to the behaviour; 3) the mechanism of pile-soil-pile system, especially about how the load is allotted to each pile, how the migration of excess pore water pressure occurs, migrates and dissipates, and how the uneven settlement is caused.