With an established convection-dispersion model for the thermal transport in aquifer, the thermal transport processes in an unconfined aquifer of a Groundwater Heat Pump (GWHP) system in Chengdu, China, are simulated with double-well intervals and cooling-load design fluctuations in summer running period under special groundwater flow and heat source conditions, and the stage-characteristics of the thermal transport in the aquifer are investigated in the running cycle (1 year) numerically. The results show that the thermal transport in the aquifer is closely related to the distance between pumping and injecting wells and the cooling-load design fluctuations, especially, to the cycling water volume. The thermal transport in the aquifer sees different characteristics in the two states in the pumping-recharging stages in summer/winter and the storing stages in spring/autumn. With the hydro-geologic theory and the numerical model, the effect of the groundwater-flow on the thermal transport in the unconfined aquifer is discussed. With an established convection-dispersion model for the thermal transport in aquifer, the thermal transport processes in an unconfined aquifer of a Groundwater Heat Pump (GWHP) system in Chengdu, China, are simulated with double-well intervals and cooling-load design fluctuations in summer running period under special groundwater flow and heat source conditions, and the stage-characteristics of the thermal transport in the aquifer are investigated in the running cycle (1 year) numerically. The results show that the thermal transport in the aquifer is closely related to the distance between pumping and injecting wells and the cooling-load design fluctuations, especially, to the cycling water volume. The thermal transport in the aquifer sees different characteristics in the two states in the pumping-recharging stages in summer / winter and the holding stages in spring / autumn. With the hydro-geologic theory and the numerical model, the effect of the groundwater-flow on the thermal transport in the unconfined aquifer is discussed.