The present study aims to reveal the influence mechanism of organic sulfur structures and microwave frequency on its dielectric property and establish the relationship between the dielectric properties of organic sulfur components in coal and the efficiency of microwave desulfurization. Results showed that the different polarization mechanisms of organic sulfur compounds lead to the real part of complex permittivity decreased initially and then increased with increasing frequency. At the same time, the real parts of the complex permittivity of mercaptan and thioether compounds were higher than that of thiophene, which were caused by their different structures. As the frequency increased, the loss tangent, microwave penetration depth, and absorption index showed decline in oscillation. The loss tangent was mainly related to the polarization mechanism; both polarization mechanism and microwave wavelength had effect on the changes of microwave penetration depth and absorption index. Mercaptan and thioether compounds were more effective at converting microwave energy into heat energy. After microwave processing, the relative content of mercaptan (thioether) in GZ, CQ, and SX coals decreased from 37.38%, 36.93%, and 40.02% to 27.34%, 29.26%, and 26.67% and of thiophene increased from 47.61%, 53.35%, and 49.54% to 58.76%, 59.09%, and 60.38%.