During hot-dry rock geothermal exploitation, granite wellbore walls are subjected to numerous thermal-cooling cycles. This exposure results in a deterioration of pore-permeability properties and poses potential risks of instability and collapse. To address this issue, nuclear magnetic resonance (NMR) techniques were employed to investigate the evolution of granite pore size, quantity, and distribution under various cooling strategies and thermal cycling frequencies, with practical drilling engineering and fluid types taken into consideration. The results indicate that pore connectivity was significantly enhanced by thermal cycling, leading to an increase in pore numbers and sizes, with a particularly notable growth in the proportion of larger pores. The porosity of granite was observed to gradually increase with the number of cycles, characterized by an initial rapid rise, followed by a slower growth rate, until ultimately stabilizing. The influence of subsequent thermal cycles on pore structure modification was diminished, which is attributed to the hindrance of heat conduction by generated thermal cracks. A notable correlation was identified between the equivalent average pore radius and the physical properties of the rock, suggesting that the alteration of granite’s pore structure following heating is the primary cause of its physical property degradation. These insights are considered crucial for the optimization of dry-heat geothermal systems.