A control method and system of an electrical vacuum pump is provide to resolve generation of peak current when a motor of the electrical vacuum pump initially starts and implement a soft start. The electrical vacuum pump generates vacuum by suctioning air by rotating a pump with a motor. The control method includes starting the motor by supplying a power supply to the motor to switch on the electrical vacuum pump and sensing current applied to the motor using a current sensing circuit. In addition, the method includes determining a target value of motor input voltage set as a value according to the sensed applied current while starting the motor until the sensed applied current reaches a predetermined current and adjusted the motor input voltage applied to the motor to correspond to the target value.