Immersed tube tunnels are usually placed on soft soil layers in cross-sea tunnelling engineering. Owing to the influence of stratum conditions and slope design, the longitudinal distribution of substratum layers is generally uneven. Thus, the inhomogeneous deformation of the element-joint becomes the key factor in the failure of the immersed tube tunnel. Therefore, a corresponding calculation method for joint deformation is needed to explore the deformation law of immersed tube tunnels. By constructing a three-section immersed tube tunnel analysis model (TTM), the relationship between the two types of deformation of the immersed tube tunnel structure in a longitudinal nonuniform soft soil foundation is described, and the deformation characteristics of the immersed structure under different boundaries are discussed. Based on the mechanical behaviour of the joint and foundation, according to the Timoshenko beam on the Vlasov two-parameter foundation (VTM), considering the tidal cyclic load during the operation and maintenance period, an example analysis is given. Moreover, the deformation characteristics and development trend of the immersed tube tunnel under the influence of different soil layers are discussed. The obtained results have a certain guiding significance for the deformation calculation of immersed tube tunnels.