The properties of SBS modified bitumen waterproof membrane (SMBM) will deteriorate under the action of heat. In this paper, SBS modified bitumen (SMB) and SMBM were aged at 80 °C for different times (0,10,20,30,40 days). The low temperature flexibility, softening point, viscosity and mass changes ratio of SMB and mechanical properties of SMBM before and after aging were tested, the microstructure and chemical structure of SMB were investigated by fluorescence microscope (FM) and Fourier transform infrared spectroscopy (FTIR). The results show that the low temperature flexibility, softening point and viscosity of SMB decrease significantly at the initial stage of heat aging (10 days), especially the influence of heat aging on the low temperature flexibility and viscosity of SMB is more obvious, and their properties degradation rate slowdown in the later stage of aging. The mass changes ratio of SMB first decreases and then increases with aging time. FM shows that the network crosslinking structure of SMB is destroyed gradually with the extension of aging time. The network crosslinking structure disappears after 40 days of heat aging. FTIR shows that carbonyl and sulfoxide compounds are increasing after aging, more carbonyl compounds than sulfoxide compounds are formed after aging for 10 days, and the degradation rate of SBS decreases. The maximum tension of SMBM first increases and then decreases, the elongation at maximum tension decreases with aging time.