An accurate prediction for deep-buried ground heat exchangers (DBGHEs) is the premise for efficient utilization of geothermal energy. Due to the complexity of the geological composition spanning thousands of meters, the configuration of boundary conditions plays a critical role in evaluating DBGHE thermal performance. This paper proposed a three-dimensional model of full-scale DBGHE involving both conductive and convective heat transfer in aquifuge and aquifer layers. The constant inlet temperature and constant heating power boundaries in the DBGHE domain, and the surface–bottom temperature and heat flux boundaries in the rock-soil domain were examined. It was found that the differences in the performance prediction caused by different DBGHE boundary conditions were closely related to the system’s operating time. The relative differences in heat extraction amount and average borehole temperature of 2000 m DBGHE caused by the two inlet boundaries on the 30th day were, respectively, 19.5% and 18.3%, while these differences on the 120th day were decreased to 8.4% and 9.9%, respectively. It was found that the constant inlet temperature boundary was more appropriate than the constant heating power condition for estimating aquifer effects on the performance of DBGHE. For the rock-soil domain, the results showed that the heat extraction amount of DBGHE under the heat flux boundary was 12.6%–13.6% higher than that under the surface–bottom temperature boundary. Particularly, when considering the velocity change of groundwater in the aquifer, the relative difference in heat extraction amount increments caused by the two types of rock-soil boundaries can reach 26.6% on the 120th day. It was also found that the thermal influence radius at the end of a heating season was hardly affected by either the DBGHE inlet or rock-soil domain boundary conditions.
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