The present disclosure relates to a fan system and a fan driving method. The fan system includes a first fan and a second fan, which are used to operate according to a first driving signal and a second driving signal, respectively, and to generate a first rotating speed signal and a second rotating speed signal. The first rotating signal has a first phase, and the second rotating signal has a second phase. The second fan is electrically connected to the first fan to receive the first rotating speed signal, and obtain a detected phase difference between the first phase and the second phase. The second fan is further configured to selectively increase or decrease the duty cycle of the second driving signal according to the detected phase difference, so that the second phase is adjusted to maintain a preset phase difference with the first phase.