Abstract: The 3D finite element modeling based on the stratum-structure method is highlighted to analyze the settlement of immersed tunnels and the opening displacement and shear deformation of joints. Several problems are discussed, such as the balance of the initial geostress, the simulation of the construction sequence, the constitutive model of the materials and the simulation of the contact relation. The feasibility of this method is verified through the project of Hong Kong-Zhuhai-Macao immersed tunnel. The balance effect of the initial geostress, the settlement of the whole tunnel and the relative displacements of the joints are studied. The following conclusions are drawn: (1) The soil stress is approximate in proportion to the burial depth, and the displacement is almost 0 after the balance of the initial geostress. (2) The maximum increment of the settlemnt of Hong Kong-Zhuhai-Macao immersed tunnel is about 9.6 cm when the back silting soil is 20 m in depth. The dredging under the ship lanes displays obvious resilience, and the sphere of influence is about 1 tube far.