Abstract: Clay soil layers are important components of the aquifer system which play important role as a water barrier insulation over the aquifer layers. However, there are few studies that quantitatively reveal the effect of clay soil layers on groundwater-source heat pump system. Based on the theory of groundwater seepage and heat transfer in porous media, a three-dimensional coupled numerical model of groundwater and heat transfer is established. Taking a groundwater-source heat pump system project in Nantong as a case study, the temperature evolution law of the aquifer layers and overlying clay soil layers under different utilization of temperature differences and circulating water volumes operating conditions are simulated to calculate the increment of internal energy in the aquifer layers and overlying clay soil layer and reveal the process of heat loss from aquifer to the overlying clay soil layers. The results indicate that clay soil layers have the characteristics of low permeability and low thermal conductivity. But it is not an insulation layer and the heat in the aquifer layers will be transferred to the clay soil layers. Heat loss accumulates continuously as the system operates and the heat in the clay soil layers cannot be recovered by pumping groundwater.