The present invention relates to a fan control system. The fan control system includes a first micro controller, a second micro controller and a first logic circuit. The first micro controller provides at least one first control signal. The second micro controller is connected to the first micro controller. The second micro controller detects operational status of the first micro controller, and provides at least one second control signal. The first logic circuit receives the first control signal and the second control signal to process logic operation and to generate at least one driving signal to fan. The fan control system of the invention utilizes two micro controllers, when one of the two micro controllers malfunctions, the first logic circuit allows the other micro controller to continue proper operation of the fan, thereby preventing the problem of insufficient heat dissipation that results from malfunction of the single micro controller of a conventional fan control system.