A low-pin count fan speed control system and a method thereof include primarily an activation unit to drive a fan to operate. When the fan starts completely, the fan slows down to a pre-determined rotation speed through an idle speed regulation unit. After achieving a pre-determined temperature through a temperature transition unit, the fan speed beings to increase from the idle speed. When the fan is operating, the rotation speed is properly increased in proportion to the temperature, using a positive temperature regulation slope unit. Therefore, through this method, the rotation speed will not be decreased by foreign objects when the fan is operating and a computer host can be provided with proper heat dissipation.