The invention relates to a pulse wind tunnel operation control system and pulse wind tunnel operation control method. The system comprises a PLC module, a driving section inflation valve, a driving section deflation valve, a driving section pressure sensor, a 1/2 valve, a double film section deflation valve, a double film section pressure sensor, a driven section inflation valve, a driven section deflation valve, a driven section pressure measuring module, a driven section vacuum pumping valve, a test section deflation valve, a test section vacuum pumping valve, a test section pressure sensor and a vacuum machine tool; the PLC module achieves automatic control in a wind tunnel test process, a distributed control mode is adopted, all operation is completed in a test control room, there is need to enter a field for work, a high pressure air source is isolated, and the personnel operation safety is guaranteed.