In order to reduce the content of sulfur and ash in coal, improve the desulfurization and deashing rates, a combined experiment method of microwave magnetic separation-flotation was proposed for raw coal. The desulfurization and deashing rates of three experiment methods, namely, single magnetic separation, microwave magnetic separation, and microwave magnetic separation–flotation, were compared. Taking the microwave magnetic separation–flotation experiment method as the main line, the effects of the microwave irradiation time, microwave power, grinding time, magnetic field intensity, plate seam width, foaming agent dosage, collector dosage, and inhibitor dosage on desulfurization and deashing were discussed, and the mechanism of microwave irradiation on magnetic separation and flotation was revealed. The results show that under the conditions of a microwave irradiation time of 60 s, a microwave power of 80% of the rated power (800 W), a grinding time of 8 min, a plate seam width (the plate seam width of a magnetic separator sorting box) of 1 mm, a magnetic field intensity of 2.32 T, a foaming agent dosage of 90 g/t, a collector dosage of 2125 g/t, and an inhibitor dosage of 1500 g/t, the desulfurization and deashing effect is the best. The desulphurization rate is 76.51%, the sulfur removal rate of pyrite is 96.50%, and the deashing rate is 61.91%. Microwaves have the characteristic of selective heating, and the thermal conductivity of organic matter in coal is greater than that of mineral. Microwave irradiation can improve the reactivity of pyrite in coal, pyrolyze pyrite into high-magnetic pyrite, improve the magnetic properties, and improve the magnetic separation effect. Therefore, microwave irradiation plays a role in promoting magnetic separation. Through microwave irradiation, the positive and negative charges in coal molecules constantly vibrate and create friction under the action of an electric field force, and the thermal action generated by this vibration and friction process affects the structural changes in oxygen-containing functional groups in coal. With the increase in the irradiation time and power, the hydrophilic functional groups of –OH and –COOH decrease and the hydrophilicity decreases. Microwave heating evaporates the water in the pores of coal samples and weakens surface hydration. At the same time, microwave irradiation destroys the structure of coal and impurity minerals, produces cracks at the junction, increases the surface area of coal to a certain extent, enhances the hydrophobicity, and then improves the effect of flotation desulfurization and deashing. Therefore, after the microwave irradiation of raw coal, the magnetic separation effect is enhanced, and the flotation desulfurization effect is also enhanced.