The invention discloses a fluorine pump system and a control method thereof. A condenser is a double-coil heat exchanger and comprises a condenser coil A and a condenser coil B; the compressor, the condenser coil A, the electronic expansion valve and the intermediate heat exchanger form a first refrigeration cycle, the indoor terminal, the electric flow regulating valve III, the intermediate heat exchanger, the electric flow regulating valve II, the liquid storage tank and the refrigerant pump form a second refrigeration cycle, and the first refrigeration cycle and the second refrigeration cycle exchange heat in the intermediate heat exchanger; and the indoor tail end, the electric flow regulating valve IV, the condenser coil pipe B, the electric flow regulating valve I, the liquid storage tank and the refrigerant pump form a third refrigeration cycle. The refrigerant in the first refrigeration cycle of the intermediate heat exchanger is separated from the refrigerant at the tail end in the supply chamber, so that the oil return problem of the refrigeration system under the conditions of long pipeline and height difference is solved, and higher applicability is achieved; meanwhile, the system has three operation modes, a compressor or a natural cold source can be used according to different working conditions, and energy consumption is reduced.