Reasonable estimates of tunnel lining dislocations in the operation stage, especially under longitudinal differential settlement, are important for the design of waterproof gaskets. In this paper, a modified shell-joint model is proposed to calculate shield tunnel dislocations under longitudinal differential settlement, with the ability to consider the nonlinear shear stiffness of the joint. In the case of shell elements in the model, an elastoplastic damage constitutive model was adopted to describe the nonlinear stress-strain relationship of concrete. After verifying its applicability and correctness against a full-scale tunnel test and a joint shear test, the proposed model was used to analyze the dislocation behaviors of a shield tunnel in Shanghai Metro Line 2 under longitudinal differential settlement. Based on the results, when the tunnel structure is solely subjected to water-earth load, circumferential and longitudinal joint dislocations are all less than 0.1 mm. When the tunnel suffers longitudinal differential settlement and the curvature radius of the differential settlement is less than 300 m, although maximum longitudinal joint dislocation is still less than 0.1 mm, the maximum circumferential joint dislocation is approximately 10.3 mm, which leads to leakage and damage of the tunnel structure. However, with concavo-convex tenons applied to circumferential joints, the maximum dislocation value reduces to 4.5 mm.