Abstract: To address the pronounced soil thermal imbalance and the decline in heating performance of heat pump units caused by the long-term operation of ground source heat pump (GSHP) systems in flower greenhouses, this study proposed a photovoltaic/thermal-couple ground source heat pump (PV/T-GSHP) system with a cross-season zonal heat storage mode. By developing coordinated scheduling strategies for different sections of the buried pipe network and various thermal storage periods, multiple cross-season zonal heat storage operational modes were designed and simulated over a 20-year cycle. Finally, an in-depth analysis of the operational characteristics was conducted for the no thermal storage, year-round full-zone thermal storage, and various cross-season zonal heat storage modes. The study first calculated the annual soil thermal storage requirement by simulating system operation under a no thermal storage mode. Subsequently, the installation area for the PV/T modules was determined according to relevant design standards. A 20-year simulation of the year-round full-zone thermal storage mode was then conducted. The results, including soil temperature, heat pump coefficient of performance (COP), and the coefficient of performance of the system (COP_sys), were compared against the no thermal storage baseline. The analysis confirmed that integrating PV/T components effectively resolved the issues of significant soil thermal imbalance and the degradation of the heat pump's heating performance, while simultaneously enhancing the overall system performance. Furthermore, it was verified that an increase in soil temperature is beneficial for improving the heat pump's coefficient of performance for heating (COP_h). Building on the premise that the cross-season zonal heat storage mode regulates soil temperature, multiple operational modes were established and simulated over 20-year periods. Comparative analysis between the year-round full-zone thermal storage mode and various established cross-season zonal heat storage modes was conducted, examining soil temperature, COP_h, coefficient of performance for cooling (COP_c), mean annual coefficient of performance (COP_m), mean annual coefficient of performance of the system (COP_msys), solar fraction (S_F), and operating costs. The results demonstrated that cross-season zonal heat storage modes can further enhance the operational performance of PV/T-GSHP systems. The optimal heat storage mode was ultimately identified as follows: the entire buried pipe field provides heating and cooling sources throughout the year. Full-zone thermal storage is implemented during the cooling season, while cross-season zonal heat storage-utilizing half of the total buried pipe area-is applied during the transitional seasons (spring and autumn) and the heating season. This configuration, while meeting cooling demands, leads to a decrease in COP_c but prioritizes the improvement of COP_h and COP_msys to the greatest extent possible. After 20 years of simulated operation under this optimal heat storage mode, the COP_m and the COP_msys increased by 7.4% and 48.4%, respectively, compared to the no thermal storage mode. When compared to the year-round full-zone thermal storage mode, the COP_msys and S_F increased by 7.9% and 7.6%, respectively. The total operating costs were reduced by 38.4% and 4.3% compared to the no thermal storage mode and the year-round full-zone thermal storage mode, respectively. The payback period for the initial investment in PV/T was shortened by 7.3% compared to the year-round full-zone thermal storage mode. Energy consumption analysis demonstrated that when the net electricity consumption (total consumption minus PV/T generation) was converted into equivalent coal consumption, the optimal heat storage mode reduced coal consumption by 50.5% and 6.8% compared to the no thermal storage mode and the year-round full-zone thermal storage mode, respectively. This study provides a valuable reference strategy for achieving more efficient and energy-saving operation of PV/T-GSHP systems in flower greenhouses. Additionally, to reduce the initial investment in PV/T and further shorten the payback period, subsequent research is recommended to optimize the installation area, tilt angle of the PV/T modules, and the system's circulating water flow rate.