In densely inhabited urban areas, deep borehole heat exchangers (DBHE) have been proposed to be integrated with the heat pump in order to utilize geothermal energy for building heating purposes. In this work, a comprehensive numerical model was constructed with the OpenGeoSys (OGS) software applying the dual-continuum approach. The model was verified against analytical solution, as well as by comparing with the integrated heat flux distribution. A series of modeling scenarios were designed and simulated in this study to perform the DBHE system analysis and to investigate the influence of pipe materials, grout thermal conductivity, geothermal gradient, soil thermal conductivity, and groundwater flow. It was found that the soil thermal conductivity is the most important parameter for the DBHE system performance. Both thermally enhanced grout and the thermally insulated inner pipe will elevate the outflow temperature of the DBHE. With an elevated geothermal gradient of 0.04 °C m−1, the short-term sustainable specific heat extraction rate imposed on the DBHE can be increased to 150–200 W m−1. The quantification of maximum heat extraction rate was conducted based on the modeling of 30-year-long operation scenarios. With a standard geothermal gradient of 0.03 °C m−1, the extraction rate has to be kept below 125 W m−1 in the long-term operation. To reflect the electricity consumption by circulating pump, the coefficient of system performance (CSP) was proposed in this work to better quantify the system efficiency. With the typical pipe structure and flow rate specified in this study, it is found that the lower limit of the DBHE system is at a CSP value of 3.7. The extended numerical model presented in this study can be applied to the design and optimization of DBHE-coupled ground source heat pump systems.