The invention relates to an arrangement method of waste water cyclone separating system in desulfurization system, and is characterized in that when a static pressure produced by the difference between a gypsum slurry cyclone overflow and a waste water cyclone inlet elevation can get over the summation of the waste water cyclone inlet pressure and a pipe water head loss, a waste water feeding box and a waste water feeding pump are removed; when the static pressure produced by the difference between the gypsum slurry cyclone overflow and the waste water cyclone inlet elevation can not get over the summation of the waste water cyclone inlet pressure and the pipe water head loss, the waste water feeding box and the gypsum slurry cyclone overflow can be connected with each other, and are arranged on a building floor with same high elevation, the waste water feeding pump and the waste water cyclone are arranged on a building floor with same low elevation or the gypsum slurry cyclone, the waste water feeding box and the waste water feeding pump are connected with each other in turn, and are arranged on a building floor with same high elevation, and are connected with the waste water cyclone arranged on the building floor with low elevation; the beneficial effect of the invention is that the design is simplified, the investment on equipment, the operation cost are reduced.