The invention relates to an apparatus for controlling an alternator of a vehicle and a method thereof. According to the method for controlling the alternator of the vehicle, a Pulse Width Modulation (PWM) duty cycle change rate can be changed to reach a target PWM duty cycle after completion of an initial engine stabilization. According to the method, PWM duty cycle is increased using an initial rate received from an ECU to prevent an engine overload from occurring when a current PWM duty cycle is less than a predetermined reference duty cycle. When the current PWM duty cycle becomes higher than the predetermined reference duty cycle, PWM duty cycle change rate can be adjusted to flexibly suppress engine RPM fluctuation and vibration in real time and to improve a response speed of an alternator output voltage.