An apparatus for controlling a motor system of an environment-friendly vehicle includes a tilt angle sensor to measure a driving tilt angle of a vehicle; a hill hold determinator to calculate a real-time driving gradient of the vehicle in order to determine a hill hold situation based on tilt angle information from the tilt angle sensor; and a variable switching determination controller to calculate a command torque for a motor based on the real-time gradient calculated by the hill hold determinator and to determine a variable switching condition of an inverter based on the command torque, a motor speed and previous and current tilt angle information from the tilt angle sensor.