As a widely used plastic, the aging and degradation of polyethylene (PE) are inevitable problems, whether the goal is to prolong the life of PE products or address the issue of white pollution. Molecular simulation is a vital scientific tool in elucidating the mechanisms and processes of chemical reactions. To obtain the distribution and evolution process of PE’s thermal oxidation products, this work employs the self-consistent charge–density functional tight binding (SCC-DFTB) method to perform molecular simulations of the thermal oxidation of PE with different crystallinity and branched structures. We discovered that crystallinity does not affect the thermal oxidation mechanism of PE, but higher crystallinity makes PE more susceptible to cross-linking and carbon chain growth, reducing the degree of PE carbon chain breakage. The branched structure of PE results in differences in free volumes between the carbon chains, with larger pores leading to a concentrated distribution of O2 and chemical defects subsequently formed. The breakdown of PE is slowed down when chemical defects are localized in low-density regions of the carbon chain. The specifics and mechanism of PE’s thermal oxidation are clearly revealed in this paper, which is essential for understanding the process in depth and for the development of anti-aging PE products.