The formation deformation caused by foundation pit excavation of soft clay is closely related to time, and using existing methods that ignore time effects to calculate the response of the tunnel below the pit bottom will underestimate its deformation. Zoned unloading is an effective measure commonly used in engineering to control the deformation of the tunnel under the principle of spatiotemporal effect. However, when evaluating the zoning effect in the current project, only the spatial effect of unloading is considered while the time effect is ignored. Firstly, the effect of soil consolidation and creep on the deformation of the shield tunnel below during the zoned unloading of the foundation pit in soft clay layer and the necessity of considering the time effect were discussed by comparing the three-dimensional finite element numerical simulation with the measured data of a foundation pit case in Hangzhou. Afterwards, the Mindlin solution was used to determine the vertical additional load at the tunnel generated by the zoned unloading of the excavation, and the subgrade reaction coefficient, which can consider the time effect of soft clay, was introduced. The existing tunnel is regarded as Timoshenko beam placed on the Pasternak foundation, and the additional load caused by the excavation was applied to the tunnel. By superimposing the deformation of the tunnel in each zoned excavation condition, a semi-analytical solution for the response of the underlying existing tunnel caused by soft clay excavation considering zone unloading and time effect was obtained. Finally, the solution was implemented in a practical example, and the applicability of the solution is verified by comparing measured data with numerical simulation results. The results show that: the deformation of the underlying tunnel induced by excavation of soft clay foundation pit is closely related to time, and the timeliness of the main consolidation caused by the dissipation of negative pore pressure and the creep of soil skeleton cannot be ignored. The attenuation of the subgrade coefficient with time is not considered in the existing two-stage analysis method, while the proposed method can better reflect the interaction process between tunnels and soft clay foundations. Under the premise of the same speed of excavation, zoned pouring bottom plates and applying reverse pressure load, the strip-block type zoning unloading scheme with small area and strip direction perpendicular to the tunnel axis below is more conducive to control tunnel deformation.