Large-scale ground source heat pump (GSHP) systems are increasingly used for space heating and cooling. In comparison with smaller ones, large GSHP systems are often coupled with much more borehole heat exchangers (BHEs). Because of the intense thermal interactions between BHEs, they are more susceptible to significant ground temperature changes. Meanwhile, they possess the advantage that their operational strategies can be applied with a high degree of freedom, which presents chances to alleviate intense thermal interactions. In this study, we used a new performance indicator to access the effectiveness of GSHP operational strategies on alleviating thermal anomalies. The Daxing Airport GSHP system, contains 10,497 BHEs and is the largest in the world; therefore, it was selected as the test case for performance enhancement through operational strategies. We established a 2D model to predict ground temperature changes during the 50-year operation of the BHEs. First, it was revealed that the most severe thermal anomalies in the study area mainly occurred both within and between the BHE arrays, which should be mitigated. To alleviate the thermal anomalies caused by the thermal interactions of BHEs, operational strategies were applied by adjusting the cooling/heating starting sequence, setting time-dependent thermal loads, and reallocating thermal loads according to the position of the BHEs. Our study demonstrates that only the operation strategy that adjusts the cooling/heating starting sequence is beneficial for different BHE layouts, while the operational strategy that reallocates the thermal loads depending on BHEs position may be only effective for specific BHE layouts. In addition, our new performance indicator can be used to evaluate the effectiveness of the operational strategies and determine the spacing of adjacent BHE arrays. Therefore, it benefits the operation management of BHE array and design of BHE layout, and further guarantees the sustainable operation of the GSHP system.