The high initial investment of borehole heat exchanger (BHE) prevents the popularization and application of ground-coupled heat pump system (GCHPs). As the premise of designing BHE, ground thermal properties are usually obtained using thermal response test (TRT), and parameter estimation method are applied based on homogeneous BHE model independent of geological stratification. In this paper, a multi-parameter estimation method using Bat algorithm (BA) is firstly proposed to obtain the layered rock-soil thermal properties based on the numerical layered BHE model, considering the characteristics of geological stratification. Then, a TRT experimental platform of three-layer BHE is developed to measure thermal responses of different stratified subsurface. Finally, the six thermal properties are obtained by the proposed multi-parameter estimation method based on BA, and their accuracy is validated using the experimental data in TRT. The five temperatures obtained from the numerical layered BHE model using the estimated results are compared with the corresponding experimental data, the results show that the maximum error of the inlet and outlet water temperatures of the BHE is respectively 3.32 % and 3.59 %, and it is 3.31 %, 2.38 % and 2.7 % for the coarse sand, fine sand and brown soil, respectively.