To deeply understand the formation mechanism of polybrominated dibenzo-p-dioxins/furans (PBDD/Fs) in the thermal disposal process of polybrominated diphenyl ether (PBDE)-containing waste, this paper studied the formation pathways of key intermediates (free radicals, FRs) in the formation process of PBDD/Fs. BDE-209, the most common PBDE in the environment, was selected as the object of study to analyze FR formation by simulating the key conditions such as temperature (850 °C) and Fe-based materials when PBDE-containing waste entering cement kiln precalciner. Electron paramagnetic resonance (EPR) spectroscopy and density functional theory (DFT) calculations were used to study the reaction. The result of simulation experiments revealed carbon-centered radicals, and DMPO-OH analysis further confirmed the generation of FRs. The findings confirmed previous calculations predicting the existence of radical intermediates during the formation of PBDD/Fs from BDE-209. DFT calculations revealed the existence of an inner ortho-position CBr bond in BDE-209. The priority order of the bond breaking of BDE-209 was ether bond, inner ortho-position CBr bond, and outside ortho-position CBr bond. BDE-209 can further form three kinds of FRs, namely, oxygen-centered radicals of single benzene rings, carbon-centered radicals of single benzene rings, and carbon-centered radicals of double benzene rings. The specific processes of FR formation were inferred: high-temperature homogeneous cleavage of chemical bonds, electron transfer, and chemisorption, where electron transfer and chemisorption may be more important pathways. The proposed inner ortho-position cleavage within BDE-209 provides new insights into the degradation of PBDEs and the formation of PBDD/Fs; the results regarding BDE-209 generation radicals further elucidate the synthesis mechanism of dioxins, which is important for controlling dioxin generation and emission during the treatment and disposal of waste containing PBDEs.