Abstract: Excavation of the overlying soil inevitably induces soil unloading effects, which further trigger deformation and internal force responses of the underlying shield tunnels. Most existing studies primarily focus on conventional-diameter tunnels (diameter D ≤ 6.6 m) with a non-zero soil cover clearance. To investigate the mechanical responses and protection measures of large-diameter shield tunnels subjected to overlying excavation with zero clearance, this study takes the segment removal project of the Jingu Haihe Tunnel at the shaft of Line B3 of the Jinan-Weifang High-speed Railway shield tunnel as the engineering background. Three-dimensional numerical simulations are adopted to analyze the influences of different excavation methods on the stress and deformation of the tunnel, as well as the control effects of various reinforcement measures. The results show that the crown heave displacement of the tunnel induced by full-depth excavation, layered excavation and slope excavation all follows a Gaussian symmetric distribution, and the longitudinally affected zone of the tunnel is approximately 2.5 times the excavation width. Excavation leads to tension on the outer side of the tunnel crown, and the distribution of additional bending moment presents an overall mountain-shaped pattern. Enhancing soil strength is more effective than improving the local stiffness of tunnel structures in mitigating the unloading effect of surrounding soil; meanwhile, the influenced region of the stratum changes from a gourd shape to a cup shape. The combined measures of end soil reinforcement and steel grid reinforcement were ultimately adopted. These measures reduced the heave displacement of the tunnel at the shaft junction to below the warning value of 10 mm, and decreased the maximum additional bending moment of the tunnel outside the shaft by 72.6%. Field application results show that the maximum tunnel heave is merely 3.8 mm. The transverse and longitudinal steel grid reinforcement technology can effectively control the longitudinal differential settlement of adjacent tunnels during shaft excavation and tunnel demolition. It also improves the tunnel’s resistance to progressive failure under extreme conditions such as water and sand leakage, thereby preventing water and sand inrush disasters.