The present disclosure relates to a fan system and a fan driving method. The fan driving method includes the following steps: transmitting a first control signal to a first fan and a second fan by a processor; determining whether a first control frequency of the first control signal is within a first frequency band and a second frequency band, wherein the first frequency band and the second frequency band are different; when the first control frequency is within the first frequency band, adjusting a first rotation speed of the first fan according to the first control signal; and when the first control frequency is within the second frequency band, adjusting a second rotation speed of the second fan according to the first control signal.