Understanding fluid flow and heat transfer in fractured rock masses is essential for advancing geothermal energy recovery. Fluid flow and heat transfer in single fractures, considering mechanical effects such as normal and shear displacements, have been extensively studied, yet the behavior in deformable intersected fractures remains underexplored. This study demonstrates, for the first time, heat transfer characteristics in intersected fractures under varying mechanical conditions, focusing on the effect of shear displacement. We first develop a computational model to simulate the shear behavior of intersected fractures under varying mechanical boundary conditions, validated against laboratory shear tests conducted in the present study. We then simulate fluid flow and heat transfer processes in the intersected fractures after shear. The results show that increasing shear displacement shifts the fracture intersection, leading to a significant rise in the cumulative energy proportion at the outlet of main flow fracture—from 63.1% to 96.5% as shear displacement increases from 0.5 mm to 5 mm. Furthermore, overlooking the effect of Constant Normal Stiffness (CNS) conditions in geothermal simulations of deep fractured rock masses could lead to an overestimation of production energy. These findings enhance the understanding of heat transfer behavior in natural fractured rock masses, contributing to more efficient geothermal energy extraction.