The invention discloses a three-stage countercurrent evaporation salt separating system for high-salt wastewater and a salt separating method thereof. The system comprises a storage tank, a preheater,a condensed water tank, a first heater, a first evaporation chamber, a second heater, a second evaporation chamber, a third heater, a third evaporation chamber, a steam condenser, a vacuum pump, a first concentrator, a first centrifugal machine, a first mother liquor tank, a flash chamber, a second concentrator, a second centrifugal machine and a second mother liquor tank, by adopting a process of combining three-stage countercurrent evaporation sodium salt separating and flash evaporation cooling potassium salt separating with opposite flow directions of steam and materials, the discharge temperature is high, the problem that the low discharge temperature is not beneficial to sodium-potassium separating is solved, and the problem of coprecipitation of potassium chloride and sodium chloride is solved by controlling the concentration of discharged potassium chloride.