The invention discloses a method and equipment for separating, conveying and filling underground coal and gangues. The method includes crushing and separating the coal and the gangues directly in an underground environment twice by a roll crushing separator and a hammer crushing separator; directly feeding separated coal briquettes into an underground coal bunker by a pneumatic conveying and filling system; crushing separated gangues into gangue fragments by a roll crusher; and conveying the crushed gangues to a mined-out region to fill the mined-out region. The method and the equipment have the advantages that the problem in the aspect of transportation for underground coal and underground gangues is solved, underground space is saved, large quantities of raw materials are provided for filling the underground mined-out region, problems of surface subsidence, accumulation of a gangue dump and the like are solved, and requirements on environment-friendly coal mining and environment-friendly production are met; and the method is smart in conception, the structure is reasonable, the equipment is simple, the occupied underground space is small, particularly, an underground transportation structure is changed owing to the pneumatic conveying and filling system, the underground space utilization rate is increased, coal and gangue separating equipment is good in separation effect, and the method and the equipment are wide in applicability and high in novelty in the field.