The invention discloses a stratospheric airship ballonet inflating and deflating system. An inlet and outlet port of a ballonet is connected with a heat exchanger, a sixth valve and a first draught fan. An inlet of the first draught fan is provided with a second electric heater. An outlet of the first draught fan is connected with a flute-shaped pipe through a fifth valve and further communicates with the inlet and outlet port of the ballonet through a fourth valve. An outlet B of the heat exchanger is sequentially connected with a second valve, a first electric heater and a first valve through a pipeline. An inlet C of the first electric heater further communicates with the inlet and outlet port of the ballonet through a third valve. By the adoption of the system, on the premise that normal work of the airship ballonet is guaranteed, a certain of refrigerating amount is supplied to electronic equipment in an airship cabin, meanwhile, heating of the electronic equipment in the cabin and the additionally-arranged electric heaters on the pipelines are used for heating gas, and a fault that equipment such as the valves and the draught fans in the system is frozen is avoided. The system is simple in structure and high in redundancy. The invention further discloses an inflating and deflating method for the system.