The operation economy of mid-deep ground source heat pump (MGSHP) system is significantly influenced by the operation mode of multi-borehole mid-deep borehole heat exchangers (MMBHE). However, as to now, the understanding about it is very limited and far from enough. This study explores the effects of the MMBHE different operating modes on the performance of MGSHP system, and the factors such as full boreholes operation arrangement, circulating water flow rate variation of individual boreholes, and building heating load variations during the heating season. The study analyzed the circulating water temperature variation, underground temperature field distribution and evolution, heat pump unit COP, coefficient of system performance (CSP), heat extraction of MMBHE, reverse heat transfer depth of MBHE, and power consumption. The results indicate that the operation mode of letting all boreholes operate throughout the whole heating season and reducing circulating water flow rate when the heating load is small and increasing it while the load is large is much better than other operation modes. With this kind of operation mode, the MGSHP system has the lowest power consumption. Even though the overall borehole extracts heat from the ground, the upper section of the borehole sometimes injects heat. The length of the heat release section can be effectively shortened by reducing the circulating water flow rate and decreases as the operation time extends. The reduction is most significant when all boreholes are put into operation. Reducing the circulating water flow rate when the load is small and increasing it when the load turns large can result in a reduction of >50 % in the fifth year compared to that in the first year.