The rise of groundwater levels is bound to affect the stress and deformation of metro tunnel structures, impacting their safe operation. To investigate the impact of rising groundwater levels on the structure of existing metro shield tunnels, the Gongzhufen-Xidiaoyutai section of Beijing metro line 10 was taken as a case study. The stratum in this section consists of a thick pebble layer, and the groundwater level from 2019 to 2025 has risen from below the tunnel invert to above the invert. To enhance simulation accuracy, factors such as the tunnel excavation process, the reduction in tunnel structural stiffness caused by segment joint bolts, and the tunnel-soil interaction were considered. The simulation results indicate that as the groundwater level rises, the maximum vertical displacement of the arch floor along the tunnel is -34.3 mm in 2019 and increases to 27.8 mm in 2025, signifying an overall uplift trend of the tunnel. Simultaneously, the bending moments and axial forces within the tunnel segments are altered by the rising groundwater, leading to a contraction trend in the horizontal direction and a rebound trend in the vertical direction. However, the overall tunnel deformation is still exhibited as a “horizontal oval” shape. Issues such as segment dislocation and cracking may be induced by this overall tunnel uplift combined with segment deformation, warranting further attention.