A fan control system includes a host device including a detecting unit for detecting a component so as to generate a detecting signal. The host device further includes BIOS for storing relationship information between the detecting signal and a rotational speed of a fan and for generating a rotational signal according to the detecting signal and the relationship information. The fan control system further includes a fan device including a fan and a fan driving unit for driving the fan. The fan device further includes a rotational speed modulating unit for controlling the fan driving unit to drive the fan to rotate at a second rotational speed outside a first range when a first rotational speed corresponding to the rotational signal according to the relationship information is within the first range.