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The ground thermal properties are the basic parameters for the design of borehole heat exchanger (BHE) in ground–coupled heat pump system (GCHPs), and their accuracy directly affects the economy and reliability of the heat pump system. In traditional design, ground is usually regarded as an isotropic homogeneous medium, and its thermal properties are obtained by solving the inverse heat transfer problem in BHE through in-situ thermal response test (TRT). In fact, different geological layers can be observed along the depth of BHE, and thermal physical properties of each layer are different based on the ground geological conditions. In order to investigate the effect of geological stratification on estimated accuracy of ground thermal parameters in TRT, a validated numerical layered BHE model (NLBM) is presented to simulated TRT, and the fluid temperature response is used to estimate effective ground thermal conductivity and borehole thermal resistance based on line source model (LSM). Secondly, the distributions of fluid temperature in U-pipe and heat flux of BHE along the depth are compared and analyzed based on the NLBM and the numerical homogeneous BHE model (NHBM). At last, borehole thermal resistance from the NLBM and estimated borehole thermal resistance from LSM are compared. The results show the maximum heat flux in the 3rd layer of the NLBM is 21.1% higher than that of NHBM, and the minimum heat flux in the 1st layer is reduced by 46.9% in the 100 h duration. The estimated λ LSM using the fluid temperature responses in the NLBM is 1.3% higher than the thickness-weighted thermal conductivity in the NLBM. The minimum relative error between R LSM and R b is still up to 10.45% in the duration of 100 h even though extending the duration is helpful to improve the estimated accuracy of R LSM. • A numerical layered BHE model is proposed and validated by the experiment. • The distributions of fluid temperatures are compared from the two models. • The differences of heat flux are illustrated in the two models. • Effect of geological stratification on estimated accuracy is investigated in TRT. [ABSTRACT FROM AUTHOR]