An apparatus and method for controlling a cooling fan of a vehicle are provided. The apparatus includes an information detector that is configured to detect information for operating the cooling fan and a blower assembly including a motor driving the cooling fan and a resistor adjusting a speed of the motor. A relay unit is configured to selectively supply power to the blower assembly. A connecting unit includes a high speed connector that is directly connected to the motor, a low speed connector that is connected to the motor via the resistor, and a ground connector that connects the motor to a ground. Additionally, a controller is configured to operate the relay unit based on the information detected by the information detector.