The previous studies on the heat transfer characteristics of deep borehole heat exchangers (DBHE) were mainly numerical simulations due to the high cost of in-situ experiments. The thermal boundary conditions of the wellbore used in these numerical simulations can be divided into the following three categories: (a) Robin or mixed boundary condition where a stable fluid with constant inlet water temperature flows through a coaxial tube. (b) Neumann boundary condition of constant heat flux locally or averaged as a whole through the wellbore, and (c) Dirichlet boundary condition of constant wellbore temperature. In this paper, a numerical study on the heat extraction performance of the deep borehole heat exchanger is carried out, the model is verified by comparing the obtained results with the experimental or numerical simulation results reported in the literature, and the influences of three thermal boundary conditions on heat output that varies with time were analyzed. The results indicate that the Neumann boundary condition commonly used in the analysis of shallow borehole heat exchangers are not suitable for actual DBHE. Under Dirichlet boundary conditions, the thermal disturbance radius after 120 days of continuous heat extraction is the largest. In addition, stable heat outputs under different operating parameters was obtained.