Thermally induced changes in mesocrack and the physical properties of fine-grained granite may influence their stability, transport characteristics, and performance related to various deep subsurface energy projects. In this study, granite was heat-treated at different temperatures (20°C, 100°C, 200°C, 300°C, 400°C, 500°C, and 600°C). The propagation and evolution of different types of cracks and the physical properties of the granite were quantitatively investigated, using optical observations of petrographic thin sections, P-wave velocity measurements, and permeability tests. The results show that as the temperature increased, the number and length of cracks increased, and the cracks were randomly distributed in all directions. This led to an increase in rock damage (λn) and an increase in permeability (K). In particular, when the temperature was ≥400°C, the damage rate significantly increased, and the number and length of intragranular cracks significantly exceeded the number and length of intergranular cracks. This led to changes in the permeation path, causing it to mainly travel through the interior of mineral particles. Using the inverse of P-wave velocity (VP), the dimensionless crack density (ρ) of granite was found to increase as the temperature increased, and this result was similar to the change of optical crack density (Pl). These analyses laid a reference for understanding the correlation between microcrack characteristics and macrophysical properties of granite.