To reveal the formation mechanism of urban shield tunnel leakage, the authors analyze the main types, locations, and leakage degrees of shield tunnel in some operating lines of Beijing metro. Furthermore, the mechanism and causes of shield tunnel leakage are explored using field observation, geological radar, and endoscope detection. Finally, numerical simulation is used to study the formation deformation rules and internal force characteristics of the segment structure when different leakage degrees and leakage locations occur at the segment joints. The research results show that: (1) The leakage of shield segment joints accounts for more than 60% of the primary leakage type, and the location of leakage is concentrated in the crown, with dripping and leakage being the leading cause. (2) The main internal cause of water leakage in shield tunnels is the uneven deformation of segment joints. The main external cause is the rapid rise of groundwater, resulting in some tunnels with potential leakage located below the water level. The strata around the tunnel are more likely to form water-rich bodies, increasing the risk of leakage. (3) The more severe the leakage at the shield segment joints and the closer the leakage location is to the arch bottom, the greater the dissipation value of the pore water pressure in the formation near the leakage point and the greater the surface settlement when it finally reaches stability. (4) Joints local leakage will result in minor elliptical deformation of the segment, and the overall structure will shift downward and toward the direction of the leakage point. In addition, changing in leakage location has a more significant impact on the internal force of the segment structure than the degree of leakage.