Mechanical stirring is a very important step in the process of ultra-fine coal separation. Through theoretical calculation and analysis, the necessity and influence mechanism of stirring energy input in floc flotation process are demonstrated, and the effects of stirring speed and stirring time on floccules size and ultra clean coal separation are experimentally analyzed. The floc size formed by coal particles grinded by two different ultra-fine grinding methods and the separation results of ultra clean coal were compared. The results show that there is an energy barrier peak in the interaction potential energy between particles, and the energy input of mechanical stirring endows the coal particles with the kinetic energy to overcome the energy barrier, which enables them to agglomerate under the action of hydrophobic potential energy. The smaller the particle size, the higher the input of stirring energy. With the increase of stirring speed or stirring time, the floccules size and ultra-clean coal yield increases slightly and then decreases gradually for coal particles with smaller particle size. Stronger stirring energy input is beneficial to the separation of ultra-clean coal with lower ash content. Compared with the coal samples grinded by stirring mill, the ultrafine coal pulverized by jet mill has a larger size of flocs and a higher yield and ash content of ultrafine coal.