Pyrite in fine coal was heated selectively by Microwave energy to strengthen its magnetism in this study. Then, the inorganic sulfur in fine coal (-0.5 mm) was removed using a 2 T strong magnetic roller magnetic separator. The migrating regulation of organic sulfur-containing groups and harmful elements was analyzed by employing a microwave energy-intensive process. As treatment time increased, the infrared absorption peaks of the sulfur compound were as follows: swing vibration absorption peak of C-S in the -CH2SH structure, Sulfone-based (O=S=O) asymmetric stretching vibration absorption peak, vibration absorption peak of sulfoxide (including the S=O bond), and C=S key :vibration absorption peak. The magnetic susceptibility of Weinan and Xiaoyi coal increased as time decreased. The magnetic Susceptibility then reached its optimal value at 4 min, at which point the dynamic balance of the transformation between pyrite, pyrrhotite, and meteorite pyrite was achieved. The maximum magnetic susceptibility was improved by 1 order of magnitude: The coal desulfurization rate and magnetic susceptibility of Weinan and Xiaoyi coal showed the same variation trend, with their optimal values emerging at 4 min.