Polyether ether ketone (PEEK) is a suitable thermoplastic matrix for composite materials in various industrial applications. Thermal treatment presents a promising approach for recycling high-performance engineering plastics through the recovery of valuable byproducts. This study investigated the thermo-oxidative behavior of PEEK using thermogravimetric analysis (TGA) and a customized pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) system to perform real-time analysis under oxidative atmospheres. Reactive force field molecular dynamics (ReaxFF-MD) simulations were employed to explore its chemical degradation mechanisms. TGA revealed that the initial degradation of PEEK occurred above 540 °C, highlighting its exceptional thermal stability. Oxygen lowered the degradation temperature by approximately 20 °C, leading to a distinct two-stage process. Notably, chemical structure changes were observed below 500 °C, consistent with ReaxFF-MD findings indicating oligomer formation first through main chain cleavage. Py-GC/MS analysis showed that PEEK pyrolysis generated valuable phenolic compounds, primarily phenol and p-phenoxyphenol. Dibenzofuran, along with significant production of CO2/CO and H2O were the predominant oxidation products. Py-GC/MS and ReaxFF-MD combined demonstrated that ether and ketone groups cleaved initially, with terminal phenylene-carbonyl radicals breaking more readily than phenoxy radicals, resulting in early CO release. Aryloxy radicals underwent chain cleavage, hydrogen abstraction, and hydrogen transfer reactions to form various phenolics. Oxygen attacked the main chains to form •HO2 and •OH radicals, which subsequently reacted with terminal rings through hydrogenation and hydrodeoxygenation. Ultimately, ring-opening reactions converted intermediates into CO2, CO, and H2O. These results offer insights into the thermo-oxidative behavior of PEEK and suggest potential for recovering high-value chemicals from waste PEEK composites.