In urban areas, the construction of subway tunnels is faced with complex crossing problems. The interaction of tunnels with structural deformation has not been comprehensively studied, especially in the construction of new tunnels crossing above existing tunnels. To better predict the structural deformation of the existing tunnels caused by shield excavation, this study used FLAC3D finite difference software, field monitoring, and an analytical method. A numerical model was used to simulate the influence of the shield weight, grouting pressure, and the grout hardening process on the existing tunnel. The results show that the deformation of horseshoe-shaped tunnel structure can be divided into four stages and the corresponding control measures should be taken for each stage to prevent the structural damage. Moreover, the weight of the shield can restrain the existing tunnel from floating up, but it may cause the cracking of the existing tunnel structure without internal steel support. Based on the “two-stage analysis method”, the simplified analytical method solved the additional stress and the uplift deformation in the first stage and second stage, respectively. The proposed analytical method can rapidly estimate the maximum uplift deformation of the existing horseshoe-shaped tunnel with different bending stiffness values under shield excavation.