A control device of a fan system includes a temperature sensing module, a comparing module and a driving module. The temperature sensing module senses an external temperature and generates a sensing signal according to the external temperature. The comparing module receives the sensing signal and outputs a comparing signal according to the sensing signal and a reference voltage signal. The driving module, which is electrically connected with the temperature sensing module and the comparing module, supplies a working voltage to the temperature sensing module and the comparing module, and outputs a rotating speed control signal according to the sensing signal or the comparing signal.