It is critical to determine the thermal parameters of the soil and pile before designing energy piles. A new parameter estimation method is proposed to interpret the thermal response test (TRT) data of energy piles. A cylindrical heat source model that considers the difference in the thermal properties between the soil and pile is adopted. This analytical model accurately describes the heat transfer process inside and outside the pile at the initial stage. First, a three-dimensional numerical model is established and verified by a large sandbox experiment in the literature. The numerical model is used to simulate a series of virtual TRTs. Second, the sensitivities and correlations of different thermal parameters are investigated. Based on the above analyses, a stepwise parameter estimation method combined with the pattern search algorithm is proposed to estimate the thermal resistance in the pile Rb, effective thermal conductivity ks and diffusivity as of the soil successively. The results show that the proposed method is feasible and effective for using the early-time data to estimate multiple parameters accurately. The relative errors of Rb, ks, and as are equal to 5.2%, 1.2%, and 13.3%, respectively. Finally, the influences of pile diameters and configurations on the accuracy of the estimation results are discussed in detail. Compared with the traditional slope method and parameter estimation methods based on other analytical models, this proposed method can save the time cost of TRTs and obtain more accurate thermal parameters.