A microwave control system is applied to control a working system to execute at least one predetermined assignment, and comprises a microwave control unit, a control card and a passive control unit. A microwave illuminator of the microwave control unit is applied to send a microwave signal. After receiving the microwave signal, the control card reflects a reflection signal to the microwave control unit, wakes up from a first sleep mode to enter a first awake mode, and sends a first control signal to the passive control unit. After the microwave control unit receives the reflection signal, the passive control unit wake up from a second sleep mode to enter a second awake mode, and the passive control unit transmits a second control signal in accordance with the first control signal to the working system, so as to control the working system to execute the predetermined assignment.