The changes of physical and chemical structure of coal were investigated during the spontaneous combustion latency. In order to analyze the effect of low temperature oxidation on physical structure, low temperature oxidation experiments, scanning electron microscopy (SEM) and low-pressure nitrogen gas adsorption (LP-N2GA) were performed on coal samples. The low temperature oxidation resulted in ravines and asperities on the smooth surface of the raw coal. The pore structure of coal samples changed slightly before 50 °C, and the specific surface area, pore volume and pore diameter were greatly improved at 70 °C. Data from LP-N2GA experiment was applied to assess the heterogeneities of percolation pores (D1) and the irregularities of adsorption pores (D2) on the basis of Frenkel–Halsey–Hill (FHH) theory. During low temperature oxidation, the pore structure of the coal tends to be internally evident, the inhomogeneity is reduced and the volumetric fractal dimension decreases. The evolution of active groups in coal was analyzed by in situ constant temperature Fourier Transform infrared spectroscopy (FTIR). The results show that the active groups have different reactive activities and changing trends. This paper reveals the changes in the chemical-physical structure of coal samples during the spontaneous combustion latency.