[Objective] Large-scale excavation unloading above an existing subway tunnel, resulting from activities such as river dredging and widening or foundation pit excavation, induces unloading deformation of the soil mass, which threatens the stability of the tunnel structure. Therefore, measures are required to limit the soil deformation. Given the limited research on the impact of river dredging and excavation on existing tunnels, this paper, taking the Nanjing Jiuxiang River Widening Project as a case study, investigates the impact of the reinforcement project’s foundation pit excavation on the shield tunnel under different working conditions. It also predicts the effectiveness of the reinforcement structure in suppressing tunnel uplift, thereby providing a reference for subsequent construction. [Methods] A pressure slab structure, consisting of a slab, bored piles, and a diaphragm wall, was proposed to protect the tunnel, and the preliminary design parameters and construction plan for these components were determined. Based on this, the Finite Element Method (FEM) was employed to predict the impact of the reinforcement measures on the existing tunnel section. First, a three-dimensional finite element analysis model was established based on the fundamental assumption of compatibility between tunnel displacement and soil deformation. The parameters for the reinforcement zone and the structure were determined based on engineering experience and field-measured data. Then, a finite element analysis of the vertical displacement of the tunnel segments was conducted under various working conditions, and the contour maps of segment vertical displacement were obtained. Subsequently, the longitudinal deformation of the shield tunnel was analyzed using the calculation results from the most unfavorable working condition. A curve fitting regression analysis was performed using the Gaussian function on the tunnel segment deformation to establish its longitudinal distribution pattern. Finally, a verification calculation of the internal forces within the tunnel structure was performed. [Results] (1) Working Condition 5 was identified as the most unfavorable case, with a maximum uplift deformation of the tunnel segments of 17.8 mm. (2) The tunnel’s vertical displacement peaked near the intersection of the river and tunnel centerlines. This displacement decreased rapidly as the distance from the intersection increased, diminishing to nearly zero at a distance of approximately 90 m. (3) For Working Condition 5, the maximum negative bending moment per linear meter of the tunnel segment was 179.2 kN·m with a corresponding axial force of 724 kN, and the maximum positive bending moment was 161.3 kN·m with a corresponding axial force of 556 kN. The calculated crack widths were 0.170 mm and 0.187 mm, respectively. [Conclusions] (1) The pile-wall-slab structure is proven to be effective in restraining the tunnel’s uplift deformation. (2) The performance of the pile-wall-slab structure is closely related to the excavation method of the foundation pit. Adopting a strip excavation by sections can effectively control ground disturbance and, in turn, tunnel deformation. (3) Overall ground reinforcement is significantly effective in suppressing tunnel uplift deformation, whereas the effect of using counterweights inside the tunnel is relatively limited.