The invention discloses an unmanned plane fuel battery activation control system and a control method thereof. The system and the method solve the problem of no use of external activation devices in unmanned plane fuel batteries, reduce parts in an unmanned plane system, are convenient for users to operate, and reduce the system cost. The system comprises a fuel battery stack, an unmanned plane motor, a standby lithium battery and a fan used for providing a heat radiation function for the fuel battery stack, the voltage output end of the fuel battery is provided with a voltage detection circuit, and the current output end of the fuel battery is provided with a current detection circuit; the fuel battery stack provides required voltage for the unmanned plane motor, the standby lithium battery and the fan, a management module is powered up by the fuel battery pack, and the management module is provided with five controllers; and the voltage detection circuit and a circuit detection circuit use voltage and current signal acquisition. The working characteristic of an unmanned plane is used, and the output power of the battery stack is controlled through controlling the rotating speed of the motor, so the battery stack is activated.