3,3-bis(azidomethyl) oxetane and tetrahydrofuran copolymer (PBT)-based thermosetting polyurethane is an ideal energetic elastic matrix for high-energy, low-smoke, and insensitive solid propellants used in the field of aeronautics and aerospace. Its aging during long-term storage will cause deterioration of the mechanical properties of the propellant, which will bring serious security risks when working. To explore the thermal aging mechanism, the PBT elastomer was prepared and then aged at 40 °C, 60 °C, and 70 °C. Starting from characteristic structures that affect the mechanical properties of elastomer, active groups, hydrogen bonds, chemical crosslinking, free volume, crystallization, microphase separation, and mechanical properties of the PBT elastomer during thermal aging were analyzed by fourier transform-infrared (FT-IR) spectroscopy, swelling method, positron annihilation lifetime spectrum (PALS), X-ray diffraction (XRD), dynamic mechanical analysis (DMA), and uniaxial tensile test, respectively. Here, we found that the thermal aging of the PBT elastomer was a coupling process of several aging effects and showed a segmented feature. Destruction of hydrogen bonds, degradation of urethanes and oxidative crosslinking between polyether backbones successively dominated the thermal oxidation process of the PBT elastomer. This work is of great significance for the development of antiaging technologies for the PBT propellant and lays the foundation for the establishment of a mechanical property deterioration model based on microstructure evolution.