To analyze the secondary oxidation of the active structures of pulverized coal and reduce risks of coal spontaneous combustion, free radical theory and functional group analysis were combined to study the effects of particle size and oxidation temperature on the active structure of coal molecules. This process was based on electron paramagnetic resonance (EPR) and Fourier-transform infrared (FTIR) technology. The results show that the reduction in pulverized coal particle size can enhance the secondary oxidation activity of coal and that the reactivity is the strongest when the particle size is 0.074−0 mm. The smaller the coal particle size is, the shorter the aliphatic side chain is after secondary oxidation. The reaction in which the side chain breaks to form a stable chain structure is also more intense. A smaller coal particle size also makes it easier to produce −OH after secondary oxidation, resulting in a large increase in the Average A (−OH) in the Coal 1# and Coal 3# at the minimum particle size range of 0.074−0 mm. The −C=O and −C−O− in Coal 1# with a lower metamorphic grade are greatly affected by temperature and particle size, and the consumption of −C=O during oxidation plays a dominant role in the secondary oxidation process. The −C=O and −C−O− in Coal 2# and Coal 3# are less affected by temperature and more affected by particle size, and −C−O− is the main group driving the secondary oxidation reaction.