The in-site thermal response test (TRT) is commonly applied in engineering, but it treats the complex soil with groundwater as the homogeneous soil without groundwater. Although the short-term heat transfer of the two soils may be equivalent, its impact on the long-term performance of the ground source heat pump system (GSHPS) remains to be proved. In this paper, a three-dimensional numerical simulation platform was established. Based on the platform, the equivalence of the TRT and its impact on the long-term performance of the system were analyzed. The results showed that the short-term heat transfer between the actual and equivalent conditions is similar, but the long-term performance of the GSHPS differs greatly, better in the actual condition. The difference of the heat transfer of compact clay, lightweight sand and dry shale between the actual and equivalent conditions were 2.65%, 2.75% and 3.07%, respectively. Under the actual condition of dense clay, the average cooling coefficient of performance (COP) in the tenth year is 29.01% smaller than the equivalent condition, but the average heating COP was 12.38% higher. Compared with first year, the heating COP in the tenth year under actual condition decreased by 1.67%, but 8.70% under the equivalent condition. (C) 2019 Elsevier Ltd. All rights reserved.