Taking a ground source heat pump operating in summer as a case study, the heat transfer performance of a ground heat exchanger was studied under different heat transfer mechanisms, considering stratified soil conditions and only considering thermal conduction. It was concluded that when the aquifer was located in the lower layer of stratified soil, the heat transfer performance of the ground heat exchanger is improved by 4.07%–37.24% in the most favourable case and by 4.11%–51.3% in the least favourable case when water migration in unsaturated soil and seepage in saturated soil are incorporated. The influence of aquifer position on the heat transfer performance of the vertical ground heat exchanger was also analysed. The results show that the heat transfer performance of the ground heat exchanger is improved by 1.05%–2.0% and 0.35%–1.61%, respectively, when the aquifer is located in the upper and middle layers of stratified soil rather than in the lower layer of stratified soil. Using the results of this paper to revise some existing studies that do not consider complex soil conditions, more accurate and practical conclusions can be obtained.