The invention provides a numerically-controlled machine tool waste separating device and a working method thereof, and belongs to the field of waste treatment. The device comprises a workbench, a crushing bin fixedly connected to the top of the workbench, and a second conveying mechanism, wherein a feeding port, a discharging port and a crushing mechanism are arranged on the crushing bin, a mounting frame is connected to the side of the workbench through bolts, a driving mechanism is arranged on the mounting frame, and the driving mechanism is connected with the crushing mechanism to achieve crushing; the second conveying mechanism comprises a second conveying belt and three third rotating shafts, waste scraps are conveyed through a first conveying roller, and when the iron materials move to the side, close to a third conveying belt, of the second conveying belt, the adsorption effect of a magnetic adsorption plate is gradually lost, so that the iron materials fall to the upper side of the third conveying belt, other waste materials are conveyed to the upper side of a discharging groove through a first conveying belt, the separation and conveying effect is achieved, the iron materials and other materials in the waste materials are effectively separated, the subsequent separation work is reduced, and the working efficiency is improved.