The invention discloses a nanometer flow jet cooling automobile seat and a working method thereof. The seat comprises flexible cooling boxes, a liquid storage tank, an electric pump, a heat exchanger,a pressure regulating valve and a controller. Each flexible cooling box comprises a box body, a temperature sensor arranged at the top of the box body, a high-pressure common rail pipe arranged in the box body, multiple nozzles arranged on the high-pressure common rail pipe and electronic control valves controlling the nozzles to be opened and closed; and a nanometer flow backflow opening is formed in the bottom of each flexible cooling box and connected with a heating medium inlet of the heat exchanger, a heating medium outlet of the heat exchanger is connected with the pressure regulating valve and the liquid storage tank, the liquid storage tank is connected with the high-pressure common rail pipes through the electric pump, the high-pressure common rail pipes are further connected with the pressure regulating valve, and the controller is connected with the temperature sensors, the pressure regulating valve, the electric pump and the electronic control valves. The surface of the seat can be quickly cooled.