The invention discloses an energy-storage type fluorine pump heat pipe system and a control method thereof. The energy-storage type fluorine pump heat pipe system comprises a first indoor unit, a second indoor unit, an outdoor unit, a liquid storage tank, a fluorine pump, an electric two-way valve, an electric three-way valve, a liquid pipe branch circuit, an air pipe branch circuit and a controller. According to the control method of the energy-storage type fluorine pump heat pipe system, starting and stopping of the fluorine pump, the electric two-way valve, a three-way reversing valve, the electric three-way valve and a fan are switched to achieve switching of multiple working conditions, the temperature and humidity requirement of industrial buildings can be ensured, and the thermal comfort requirement of commercial buildings can also be ensured. According to the energy-storage type fluorine pump heat pipe system and the control method thereof, a natural cold source and industrial waste heat are fully utilized, the energy utilization efficiency and the indoor comfort can be effectively improved, the night trough electricity price is utilized, and the economical operation cost is reduced.