Exploitation of deep geothermal energy based on a deep borehole heat exchanger (DBHE) system significantly promotes green and low-carbon development. The DBHE is the core apparatus of this system, and many mathematical models have been proposed to investigate its thermal performance. However, groundwater seepage which is one of the most important factors has not been considered in most previous numerical models. In addition, the temperature distribution of rock and soil with different seepage velocities during the thermal recovery period is still unclear. Therefore, to fill this research gap, there is a strong need to propose a novel numerical model for DBHEs that considers groundwater seepage and can be solved quickly. In this paper, a computationally efficient numerical model that considers groundwater seepage is proposed. Compared with the experimental data from a field test, the model’s root mean square error is 1.33 °C. Moreover, the time required for the simulation of DBHE operation for one year using this model is only 47.3 s. Then, the effects of groundwater seepage on the DBHE and rocky soil are investigated. The findings demonstrate that when the seepage velocity is high, the thermal performance of the DBHE will be underestimated if groundwater seepage is neglected. At the seepage velocities of 1 × 10-7, 3 × 10-7 and 5 × 10-7 m/s, the heat extraction rate of the DBHE increased by 4.92 %, 10.83 %, and 15.34 %, respectively, compared to the heat extraction rate of the DBHE calculated without taking the groundwater seepage into account. Furthermore, groundwater seepage can increase the temperature recovery capacity of rock and soil. The natural temperature recovery rate of rock and soil without seepage is 86.20 %, and the temperature recovery rate is 93.11 % if the seepage velocity reaches 1 × 10-7 m/s. This study provides essential theoretical guidance for DBHE system design in areas with high groundwater seepage velocities.