A structure for controlling a Y-capacitor for reducing common mode noise of an electric power conversion system of an environmentally-friendly vehicle. The structure cooperates with an infotainment system for a vehicle and reduces common mode noise of an electric power conversion system. In particular, the structure includes: a switching element connected to a high-voltage power source coupled to the vehicle and to attenuate noise occurring at the time of PWM control; and an electric power conversion part which receives common mode noise occurring from the power source and controls ON/OFF of the switching elements in order to reduce the received common mode noise.