Abstract: At present, most of the cross-sea cluster projects adopt the immersed tube tunnel, such as Hong Kong-Zhuhai-Macao Bridge and Shenzhen-Zhongshan Channel. With the completion of the projects, the long-term settlement laws during the operation and maintenance periods have gradually become the focus of research. In the settlement calculation of joints, the Euler beam model on the Winkler foundation is mostly used. However, the shear deformation of the flexible element-joint and the continuity of the foundation are ignored and the displacement of the element caused by the interaction between the element and the soil is not considered, thus the results greatly deviate from the actual ones. Considering the back silting and desilting loads during the operation and maintenance periods, based on the stress and deformation characteristics of the flexible immersed tube tunnel, the elements are equivalent to the Timoshenko beams placed on the Vlasov double-parameter foundation, the continuity of the foundation is considered, the stiffness of the soil is strengthened, and the bending and shear deformations of the elements are considered, namely, the deformation of the elements is regarded as the dislocation deformation mode. Accordingly, the formula for calculating the vertical deformation is derived. Meanwhile, the Euler beam model and the Timoshenko beam model placed on the Winkler foundation model are introduced for comparison to verify the rationality of the proposed method. Taking the Yongjiang immersed tube tunnel project as an example, the laws of the vertical displacement of the elements under the influences of back silting and desilting loads are analyzed, and the theoretical results of the above four models are compared with the observed ones. The results show that the Timoshenko beam model placed on the Vlasov double-parameter foundation has more preferable results compared with the other three methods. The settlement of the element-joint caused by back silting loads changes exponentially with time, the settlement develops rapidly at the early stage, and it decreases step by step with a half-year period at the middle and late stages. The frequency of dredging affects the settlement, and the settlement of the element-joint caused by dredging twice a year is the least. The research results may have some guiding significance for the design and operation management of the element-joint in immersed tube tunnels.