With the normalization of deep mining, the risk of residual coal spontaneous combustion (CSC) in deeply mined areas has gradually increased. To investigate the thermal characteristics and microgroup transformation mechanisms during the secondary oxidation of deep-well oxidized coal, a deep-well oxidation process was simulated in a synchronous thermal analyzer, and the thermal parameters of the oxidized coal were tested. The correlated transformation pathways of microscopic active groups was studied by electron paramagnetic resonance (EPR) and in situ diffuse reflectance (in situ FTIR) experiments during the reoxidation of oxidized coal. The results showed that with increasing deep-well ambient temperature and oxidation temperature, the characteristic temperature of coal gradually decreased, exothermic heat release gradually increased, and active aliphatic structures and -OH, -CHO and other active functional groups gradually accumulated and became distributed more uniformly. When the thermal conditions and oxidation temperature were very high (> 160 °C), the active free radicals in the oxidized coal were rapidly consumed, resulting in a gradual decrease in the characteristic temperature and heat release during the secondary oxidation process, while the contents of peroxy and carboxyl groups continued to increase. In the slow oxidation stage of oxidized coal, methyl groups were mainly transformed with hydroxyl and peroxide groups (r > 0.96), and the associated oxidative consumption of -CHO and -COOH mainly occurred in the rapid oxidation stage (r > 0.99). Geminal diols and peroxy groups are important intermediates in the coal–oxygen composite reaction process. With an increase in the deep-well temperature and initial oxidation temperature, the reoxidation tendency and heat release capacity of residual coal in the goaf gradually increased, and the risk of CSC intensified. The research results provide a theoretical reference for the prevention and control of coal fires in deep mines and play an important role in guiding environmental management and gas emissions reduction measures in mining areas.