Fine coal separation is one of the research focuses in the field of clean coal technology. A new type of fine coal dry separation technology was studied. Microwave energy was used to strengthen the magnetic properties of coal pyrite, leading to high-gradient magnetic separation. A high-intensity magnetic separator was used for the separation of fine coal, and an effective way to achieve the clean utilization of pulverized coal before its combustion was investigated. The R-2 and corrected R-2 values of the two-order model according to the sulfur content of clean coal were small. This shows that the recommended model has a higher fitting degree of response surface. Microwave pretreatment time T has a higher sensitivity to the sulfur content of clean coal than MC in a given range. The response surface has an optimal value, i.e., the highest desulfurization rate. With the increase in magnetic particle size, the desulfurization rate increased continuously. The evaluation index of the clean coal sulfur content of fine coal microwave-enhanced magnetic desulfurization test was optimized by a better two-order fitting model. The constraint conditions of the main influencing factors and the optimization indexes after the response were obtained. The sulfur content of clean coal was in the range of [1.98, 3.35].