A power factor correction (PFC) protection device used when an abnormal current of a three-phase inverter occurs and a method of controlling the same are disclosed. If any mis-connection (or non-connection) occurs due to a mistake of a producer at a power-supply input terminal applied to the reactor and the switching element, a current applied to the switching element becomes an abnormal current, such that the PFC cannot be controlled. During the PFC control, the device detects a current waveform generated from the switching element at a current sensor of the common potential terminal, and determines whether there is a mis-connection caused by the abnormal current. If the mis-connection is decided, the device compares a current pattern with a mis-connection pattern, and changes the PFC control output applied to the switching element according to the searched mis-connection pattern, such that the PFC control can be normally carried out.