This work establishes a fine model reflecting the characteristics of immersed tube structures to study the spatial mechanical characteristics of variable cross section immersed tunnels. Then, the mechanical behavior of the pipe segments under differential deformation is explored, based on which we propose a formula for estimating the shear key force and analyze the corresponding failure mechanism and failure mode. Thus, the critical points of the pipe segment design are specified. The results show that, first, the variable cross section segment bears more sectional internal force (over 47%) than the uniform cross section segment in actual cases, which should be fully considered in practical reinforcement design. Bearing deformation alternatively occurs at different shear keys, implying an apparent spatial stiffness matching problem. Second, the pipe segments show overall settlement under longitudinal bending, failing to satisfy the assumption of deformed plane sections. The force on the shear keys varies with the quadratic function of the longitudinal bending degree, and the dislocation magnitude has a positive near-linear relationship with the bending degree. Third, when subjected to torsion, the shear keys of the weak sidewalls are sheared to resist torsion. Then, this force is laterally transferred to the top and bottom plates and jointly shared by the adjacent shear keys, explaining why shear is adjusted with structural deformation. Fourth, under the action of spatial differential deformation, the shear force is mainly undertaken by the vertical shear keys. When the structure is subjected to bending, compression and shear failure occur at the end angle of the middle wall shear key, and its root junction experiences tension and shear failure. When subjected to longitudinal torsion, the local tension and shear failure at the root of the shear key on the soft subgrade side cause a joint failure. Finally, based on the bearing characteristics, failure mechanism, and failure mode of variable cross section immersed tunnels, the idea of strengthening immersed tube structures is put forward, which can guide similar engineers.