To understand the endowment characteristics of the organic sulfur in coking coal and know about the chemical mechanism of microwave to organic sulfur in coal are of great importance to the enrichment of the coal desulfurization theory, optimization of the microwave desulfurization process of coal and development of new technology of fine coal processing. XPS and XANES were used to represent the main structure types of organic sulfur and the relative content of organic sulfur in coking coal. Based on the difference of coal density characteristics, we explored the types and content changes of organic sulfur. The benzothiophene and 3-thiophenecarboxylic acid were selected for microwave irradiation experiments at 915 and 2 450 MHz. The variation characteristics of sulfur structures in the model compounds were studied by Raman spectroscopy. The quantum chemistry simulation was performed using Materials Studio to calculate different directions. Materials Studio was used to simulate the configuration parameters of model compounds under energy fields in different directions. We compared the conformation changes of the model compounds after microwave radiating, and analyzed the response mechanism of the sulfur chemical bonds in the coal to the microwave. The XPS and XANES characterization results showed that sulfur in coking coal is dominated by organic sulfur, and thiophene is the most important form of organic sulfur. With the increase of the densities of coking, thiophenic content decreases relatively, a thiol (ether), and (sub) sulfone gradually increase, and the content of three types of organic sulfur tends to be average. After applying the applied energy fields in different directions, the chemical bonds length and bond level of sulfur in benzothiophene and 3-thiophenecarboxylic acid were not obvious, indicating that the microwave energy fields have limited stretching and torsion of chemical bonds. However, there had influence on the bonds angle and dipole moment in the molecular structures of the model compounds by different energy fields application directions. Raman spectrum showed that the vibration peaks of sulfur chemical bonds in the model compounds were red-shifted after microwave irradiation at 915 and 2 450 MHz. Therefore, microwave radiation affected the local structures of the model compounds microenvironment, and changed their molecular configuration and molecular polarity. At the same time, the vibration recovery force of the crystal lattice was reduced, the interaction force between atoms was weakened, and the fracture of sulfur chemical bonds and the dissociation of sulfur were promoted. It was found that the 915 MHz microwave radiation had more obvious effects than 2 450 MHz.