The disengaging between invert filling and segment affects the safety of train operation. A 3D numerical model of a three-ring staggered assembled shield tunnel is established, which is verified by a full-scale test. On this basis, cohesive element is inserted between the invert filling and tunnel segment to simulate the fracture process of invert filling-segment interface, and explore the relationship between the deformation of staggered assembled shield tunnel and the disengaging of invert filling. The results show that: 1) The development of invert filling disengaging affects the internal forces of shield tunnel segments. 2) The relationship between the development of invert filling disengaging and the deformation of shield tunnel can be four stages. Different segment assembly methods do not affect the variability of the disengaging ratio. Tensile failure occurs in 89% of the interface layer, which is the main form of invert filling disengaging. 3) The relationship between the development of disengaging distance and the deformation of shield tunnel also can be four stages. The faster the horizontal convergent deformation develops in the segment assembly method, the slower the growth rate of the disengaging distance. 4) The faster the horizontal convergent deformation develops in the segment assembly method, the slower the growth rate of the disengaging volume.