Disclosed is a system and method of controlling an inverter to reduce noise in an eco-friendly vehicle. In the method, at least one of a current motor torque and a current motor speed is monitored in real-time. It is determined whether or not the at least one of the current motor torque and the current motor speed corresponds to a noise occurrence range set to a current switching frequency. A changed switching frequency value corresponding to the at least one of the current motor torque and the current motor speed is calculated when the at least one of the current motor torque and the current motor speed corresponds to the noise occurrence range. A PWM signal is generated using the changed switching frequency value to control an inverter.