In this paper, settlement of piled-raft foundation for high-speed train is considered systematically. It is observed in a case study that the railway settled significantly due to the cyclic train loading after a one-month trial operation. As traditional methods such as empirical methods or numerical simulation based on primitive constitutive models are unable to properly interpret the settlement mechanism, a sophisticated model-based numerical simulation, using a soil-water coupled finite element (FE)-finite difference (FD) hybrid algorithm, is conducted to investigate the mechanism of the settlement of the piled-raft foundation and excess pore water pressure (EPWP) of soft soils caused by the cyclic train loading. In order to demonstrate the performance of this numerical simulation, the calculated results are compared with the data recorded in the one-month trial operation and the reliability of the proposed numerical method is confirmed. The newly proposed numerical method is also used to predict the long-term settlement and the change in the EPWP during a one-year period. The predicted results suggest that without proper treatment, more serious settlement would have occurred, which is unacceptable in engineering terms.