The heat transfer performance of ground heat exchangers (GHEs) is influenced by different geological structures. A three-dimensional heat transfer model of GHEs was established with typical geological structures of Wuhan and Chongqing working separately as boundary conditions. Via the model calculation, their heat transfer performances were obtained and the influence of geological structures on heat transfer performances was investigated. The simulation results were validated by a practical thermal response test of a ground source heat pump (GSHP) system which showed a good match between the simulated and experimental results and could be applied to practice. The heat transfer performance and the energy-efficiency performance of GSHP systems in these two areas can be predicted with the proposed model, thus it could contribute to further research on the influence of different climate zones and geological structures on the heat transfer performance of GHEs.