Thermal treatment are commonly used to address organic contaminated soils. In particular, the pyrolysis of organic substances can result in the creation of environmentally persistent free radicals (EPFRs). We investigated a steelworks site in Chongqing (China) to observe changes in EPFRs before and after thermal treatment. Our findings revealed that the EPFRs were carbon-centered radicals with a g-factor < 2.0030 and a spin density ranging from n.d.–5.23 × 1015 spins/mg. The formation of EPFRs was driving by polycyclic aromatic hydrocarbons (PAHs), Mn, Cu, and total organic carbon (TOC). Following the thermal treatment, the spin densities of EPFRs increased by a factor of 0.25 to 1.81, with maximum levels reached at 300 °C. High molecular weight PAHs exhibited high heat capacity, enabling the generation of more EPFRs. The thermal decay of EPFRs occurred in two stages, with the shortest 1/e lifetime lasting up to 16.8 h. Raising the temperature or prolonging time can significantly reduce EPFRs levels. Thermal treatment increased the generation of EPFRs, hydroxyl radicals (•OH) and superoxide radical (•O2–), leading to a decrease in bacterial luminescence. Specifically, •OH contributed to approximately 73% of the B. brilliantus inhibition. Our results highlight that the thermal treatment significantly enhance EPFRs concentrations, and the treated soil remained ecologically risky. The knowledge of the formation of EPFRs and their biotoxicity is shedding new light on the thermal treatment risk management.