Lower borehole thermal resistance and higher heat exchange capacity are essential for enhancing BHE thermal performance in GCHP systems. The effects of different shape-stabilized phase change backfill materials (SSPCBM) on BHE performance were investigated under layered geological conditions. Numerical simulations were conducted to assess various SSPCBM deployment cases. A full SSPCBM application (b-b-b-b case) was found to reduce borehole thermal resistance by 44.37% and increase maximum dynamic heat flux by 76.6%, compared to conventional backfill. Significant variation in heat exchange improvement was observed among cases. Partial application near the inlet (a-b-a-a case) yielded a 28.1% improvement, attributed to higher fluid temperatures in the corresponding U-tube section. Phase change behavior of SSPCBM was analyzed under stratified subsurface conditions, revealing that transition rates were strongly influenced by soil thermal properties. Slower phase change was observed in Soil 3 than Soil 4, despite higher fluid temperatures. Spatial deployment effects showed that SSPCBM placement in high-conductivity layers (a-a-b-a case) caused an 18.44% reduction in thermal resistance, while placement in low-conductivity distal layers (a-a-a-b case) resulted in only a 9.92% reduction. These findings highlight that the optimal SSPCBM deployment is determined by both local thermal conductivity and fluid temperature distribution, offering practical guidance for its application in layered geological conditions.