The invention provides a fan control system and a method thereof, wherein, the system is used for controlling a fan, the fan corresponds to a slot position collection; and the system comprises a firstacquisition module for acquiring a first slot position collection, wherein, the first slot position collection is the slot position collection of a single plate meeting a heat dissipation control condition among the slot position collections; a steering determination module for determining target steering of the fan according to a position relation between each slot position in the first slot position collection and the fan; and a rotating speed control module for determining the target rotating speed of the fan according to temperature information of the single plate meeting the heat dissipation control condition. The fan control system of the invention can accordingly reduce the temperature of the single plate meeting the heat dissipation control condition, determine the target rotatingspeed of the fan according to the temperature information thereof, prevent high-speed continuous operation state of the fan and increase the service life; and by controlling steering and rotating speed of the fan, temperature of the single plate can be quickly reduced, thus reaching better temperature reduction effect and guaranteeing service transmission.