Over-crossing excavation will cause the heave deformation of existing shield tunnels and endanger the service performance of existing shield tunnels. The current analytical methods for predicting the heave deformation of a shield tunnel due to excavation always consider the shield tunnel as an elastic continuous beam resting on an elastic foundation model, which overlook the effect of the joint between adjacent rings. Thusly, a shield tunnel model with adjacent joints is proposed. The nonlinear characteristics of soil deformation are considered by nonlinear Pasternak foundation model. Through the two-stage analysis method, the simplified solutions of heave displacement and opening of shield tunnel under the action of upper span excavation of foundation pit are derived. The additional unloading pressure on shield tunnel due to excavation is calculated using MINDLIN’s elastic solution. The differential equation of heave deformation of the shield tunnel due to exerted unloading pressure is established. The heave deformation and internal force distribution of the adjacent shield tunnel caused by excavation are obtained by using the finite difference method. The measured results from three well-documented published cases are collected, and then the prediction from proposed method is compared with the measured results and the prediction from existing methods to verify the applicability of the proposed method.