Carbonization process of pyromellitic dianhydride (PMDA)-4,4′-diaminodiphenyl ether (ODA)-type polyimide has been studied for decades. However, various reaction mechanisms have been proposed and the detailed mechanisms are still controversial. It is essential to understand the carbonized structures of PMDA-ODA-type polyimide before analyzing the defect structures in graphite. In this work, the carbonization mechanisms of polyimide heated at 1273 K or lower were unveiled and the methodology to analyze carbon materials containing nitrogen, oxygen, pentagons, and heptagons using computational spectral analysis combined with molecular dynamics simulation (ReaxFF) are exhibited. For example, the formations of isoimide and cyclic ether were estimated by ReaxFF, and the presence was supported by experimental and calculated X-ray photoelectron spectroscopy (XPS) and carbon-13 nuclear magnetic resonance (¹³C NMR) spectra of polyimide heated between 813 and 873 K. The formations of pentagons and heptagon, suggested by ReaxFF, were also supported by Raman and ¹³C NMR spectra of polyimide heated between 833 and 1273 K. This work also revealed that the previously reported structures were unstable and that amine in the basal plane was the most plausible structure in polyimide heated at 1073 K or higher, as clarified by XPS, ReaxFF, and the energy calculation.