A fan control system for use in a server system is disclosed. The fan control system includes a first monitoring and protection chip, a second monitoring and protection chip, a switch, a plurality of fans and a complex programmable logic device (CPLD). In a shutdown state of the server system, the switch is switched under control of the CPLD so that the fans are connected to the second monitoring and protection chip, receive standby power therefrom and run at a standby power level. When the server system is switched to a working state, the switch is switched under control of the CPLD so that the fans are connected to the first monitoring and protection chip, receive operating power therefrom and run at a higher working power level. This design can address different heat dissipation needs of various applications.