This article studies the effects of cooling methods and aggregate sizes (particle size: 0.63–1.25 mm, 1.25–2.5 mm, 2.5–5.0 mm, 5.0–10.0 mm) on the microscopic properties and damage characteristics of cement mortar specimens. After heating the specimens to 400 °C, air cooling (cooling in air as a whole, A), water cooling (cooling in water as a whole, W), and semi-water cooling (half in air and the other half in water, AW) cooling methods are applied. The T2 spectrum, magnetic resonance imaging (MRI), permeability and P-wave velocity of the specimens were tested by low-field nuclear magnetic resonance (NMR), pulse pore permeability tester and digital acoustic wave instrument, respectively. The effect of cooling method and aggregate size on pore size distribution and fractal characteristics, permeability and tortuosity, P wave and damage degree of cement mortar specimens were studied. The relationship between MRI pixel value and damage degree was deeply explored. The results show that the average permeability and MRI pixel value increase after high temperature, and the pore tortuosity decreases. The mass loss rate, the increase of the most probable pore size and the increase of the pore volume are negatively correlated with the aggregate size, and the permeability ratio, the decrease of the tortuosity and the damage degree are positively correlated with the aggregate size. At the same time, the influence of cooling method on mass loss rate, porosity and permeability from large to small is: A, AW, W, while the decrease rate of pore tortuosity from large to small is: AW, W, A. The most probable pore size and pore volume change most obviously after high temperature treatment of W and AW. In addition, with the increase of aggregate size, the fractal dimension increases under air cooling, and the U-shaped change with W2.5 particle size as the threshold decreases first and then increases under semi-water cooling. Finally, there is a good exponential relationship between the average ratio of MRI pixel values and the damage degree, and the damage degree of the sample can be obtained by the average ratio of MRI pixel values.