The variation of physical and mechanical properties of rock after heat treatment is related to the variation of internal pore structure. In this paper, two kinds of granites treated with heating and water cooling treatment were taken as the object. Gas permeability test was carried out to study the evolution of transfer properties and changes in microscopic pore structure. The specific surface area and pore size analysis tests were used to analyze the damage evolution and the crack development of granite after heating and water cooling treatment at a microscopic level which provides a theoretical basis at a macroscopic level. The results show that two granites with different compositions show the same rules after being subjected to high temperature and water cooling. As the temperature increases, temperature cracks gradually occur inside the rock, physical properties decrease, specific surface area increases, and total pore volume increases. And the distribution of nano-scale pores in the rock can be obtained by using specific surface area and pore size analysis. It is found that the mesopores are most affected by temperature. It can be seen that the thermal cracks are one of the main factors affecting the physical properties of rocks. And specific surface area and pore size analysis tests can be used to obtain the nano-scale pore distribution inside the granite, which provides technical support for the study of the micro-pore structure of the granite.