Cooling techniques following thermal treatments and related microcracking are a hot spot in rock mechanics and must be precisely studied. Hence, this research performed systematic experiments on the influences of rapid cooling on the behavior of thermally treated granodiorite at different temperatures. Furthermore, using the optical microscope, a comparison between rapid and slow cooling methods was studied to investigate how the cooling process affected the microstructure of the Egyptian granodiorite. The granodiorite samples were heated to 200, 400, 600, and 800 °C and then cooled slowly by air and rapidly by the water. According to the experimental results, the changes in examined properties occurred in three distinct temperature stages: zone I (25–200 °C), zone II (200–400 °C), and zone III (400–800 °C). Zone II was a conspicuous transition region for the rapid cooling approach, distinguished by a significant increase in porosity, thermal damage, crack density, and a substantial decrease in wave velocities, uniaxial compressive strength, and elastic modulus. Microcrack densities and widths increased with temperature for both cooling methods. According to microscopic analyses of granodiorite samples, boundary cracks were formed at the boundaries of quartz and feldspar first due to their minimal lattice energy, followed by biotite of high lattice energy. However, due to the thermal shock induced, the intragranular microcracks of the rapid cooling technique began to form at lower temperatures (200 °C). The physical and mechanical properties of rapidly cooled granodiorite significantly dropped between 200 and 400 °C, and the failure mode altered from axial splitting to shear modes. Consequently, over 600 °C, longitudinal waves could not penetrate rock samples due to the thermal fusion of inter and transgranular fissures, which turned into macrocracks. Hence, the elastic modulus measurements and wave velocity at 800 °C were challenging with an extremely low UCS and complex failure mode.