A fan filter unit and a control method thereof are provided. The fan filter unit includes a fan and a control module. The control module includes a logic judgment circuit, a fan power supply and a control circuit. The logic judgment circuit is connected to an apparatus power supply of a semiconductor apparatus. The logic judgment circuit is used to judge whether the apparatus power supply is shut down. The control circuit is connected to the fan power supply and the logic judgment circuit. If the apparatus power supply is shut down, the control circuit switches a fan power supply path from the apparatus power supply to the fan power supply.