Aquifer thermal energy storage (ATES) system has received attention for heating or cooling buildings. However, it is well known that land subsidence becomes a major environmental concern for ATES projects. Yet, the effect of temperature on land subsidence has received practically no attention in the past. This paper presents a thermo-hydro-mechanical (THM) coupled numerical study on an ATES system in Shanghai, China. Four water wells were installed for seasonal heating and cooling of an agriculture greenhouse. The target aquifer at a depth of 74–104.5 m consisted of alternating layers of sand and silty sand and was covered with clay. Groundwater level, temperature, and land subsidence data from 2015 to 2017 were collected using field monitoring instruments. Constrained by data, we constructed a field scale three-dimensional (3D) model using TOUGH (Transport of Unsaturated Groundwater and Heat) and FLAC3D (Fast Lagrangian Analysis of Continua) equipped with a thermo-elastoplastic constitutive model. The effectiveness of the numerical model was validated by field data. The model was used to reproduce groundwater flow, heat transfer, and mechanical responses in porous media over three years and capture the thermo- and pressure-induced land subsidence. The results show that the maximum thermo-induced land subsidence accounts for about 60% of the total subsidence. The thermo-induced subsidence is slightly greater in winter than that in summer, and more pronounced near the cold well area than the hot well area. This study provides some valuable guidelines for controlling land subsidence caused by ATES systems installed in soft soils.