<p>With the continuous development of urbanization, ground surcharge will inevitably appear around subway tunnels and lead to tunnel deformation. This deformation is caused by ground surcharge in clay and continuously develops with time and space changes. Existing research has mainly considered the influence of ground surcharge on the law of short-term tunnel deformation. However, research on the temporal and spatial evolution law and mechanism of long-term tunnel deformation is lacking. This study investigated the influence of long-term tunnel deformation caused by surcharge in clay and elucidated the mechanism of long-term tunnel deformation through numerical stress analysis. The long-term deformation and stress variation of a tunnel caused by surcharge in clay were investigated from the viewpoints of the surcharge magnitude, consolidation effect, tunnel lining stiffness, and Young’s modulus of soil. The following conclusions were drawn: (1) ground surcharge causes the settlement of a tunnel in clay. The consolidation effect further increases the tunnel settlement. After 200 days of consolidation, the tunnel settlement increased by 128% compared with that immediately after the completion of surcharge loading. With the dissipation of pore water pressure, the effective stress on the tunnel gradually increased, leading to the increase of tunnel settlement. (2) The vertical compression and horizontal tension of the tunnel in the cross-section lining were caused by surcharge in clay. The consolidation effect greatly influenced the diameter deformation of the tunnel cross-section lining. The results can provide a theoretical reference for predicting and controlling the deformation of a tunnel on clay foundation in practical engineering.</p>