System and method of controlling motor for reducing vibration of electric vehicle

A system and a method of controlling a motor for reducing vibration of an electric vehicle are provided that maximize an output torque of the motor by applying a vibration reduction torque gain based on a position value of the accelerator pedal. The system includes a driving motor as a power source and an accelerator pedal position sensor configured to detect a position value of an accelerator pedal. In addition, a controller is configured to calculate a virtual position value of the accelerator pedal limited to an increasing slope or a descending slope based on the position value of the accelerator pedal, and output a final torque of the driving motor by applying a vibration reduction torque gain based on the virtual position value of the accelerator pedal.