The heat transfer performance of ground heat exchangers (GHEs) is influenced by different geological structures. A three-dimensional heat transfer model of double U-type GHEs is established with typical geological structure of Wuhan and Chongqing as boundary conditions separately. The heat transfer performances are obtained through the model calculation. The simulation results are validated by a practical thermal response test of a ground source heat pump (GSHP) system, which shows a good match between the simulated and experimental results. The influence of geological structure on heat transfer performances is investigated and the heat transfer performance of GSHP systems can be predicted. Besides, the average heat transfer coefficient of GHEs is calculated in these two area with the proposed model, and the average heat transfer coefficient of the heat exchanger is K₁=1.65 (w/m.K) in Wuhan area, K₂=1.51 (w/m.K) in Chongqing area, respectively.