The long-term settlements over tunnels can be rather significant, particularly when tunnels are embedded in soft and compressible soils. The long-term settlement can be predicted based on the stress-strain-time relationship of soft clay using multiple-step FEM. The influence of drainage condition of tunnel linings on the evolution of long-term surface settlement, as well as ground loss, are simulated with the multiple-step numerical procedure, and some conclusions are drawn from the numerical simulations. Finally, a case study is also performed and a satisfaction agreement between the predicted long-term settlement and the observed one is obtained.